PDB-9dty: Crystal structure of PRT3789 in complex with the bromodomain of h...

Basic information

• Entry: Database: PDB / ID: 9dty
• Title: Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

Components

• Elongin-B
• Elongin-C
• Isoform Short of Probable global transcription activator SNF2L2
• von Hippel-Lindau disease tumor suppressor

• Keywords: TRANSCRIPTION / SMARCA2 / VHL / PROTAC / ternary complex

Function / homology

Function:

bBAF complex / npBAF complex / nBAF complex / brahma complex / regulation of cellular response to hypoxia / GBAF complex / nucleosome array spacer activity / regulation of G0 to G1 transition / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / intermediate filament cytoskeleton / target-directed miRNA degradation / elongin complex / regulation of nucleotide-excision repair / Replication of the SARS-CoV-1 genome / VCB complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Cul5-RING ubiquitin ligase complex / positive regulation of T cell differentiation / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / positive regulation of double-strand break repair / SUMOylation of ubiquitinylation proteins / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of cell differentiation / spermatid development / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Tat-mediated elongation of the HIV-1 transcript / negative regulation of signal transduction / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / Vif-mediated degradation of APOBEC3G / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / Inactivation of CSF3 (G-CSF) signaling / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / helicase activity / negative regulation of cell growth / Regulation of expression of SLITs and ROBOs / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / cell morphogenesis / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nervous system development / Neddylation / regulation of gene expression / microtubule cytoskeleton / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / histone binding / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / protein ubiquitination / protein stabilization / cilium / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / regulation of DNA-templated transcription

Domain/homology:

BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SKP1/BTB/POZ domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase

Component:

: / ACETATE ION / CITRIC ACID / von Hippel-Lindau disease tumor suppressor / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 / Elongin-C / Elongin-B

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
• Authors: Dou, Y. / Wang, M. / Xu, C.

Funding support

1items

Organization	Grant number	Country
Not funded

• Citation: Journal: Cancer Res. / Year: 2025; Title: PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers; Authors: Hulse, M. / Wang, M. / Xu, C. / Ito, K.

History

Deposition	Oct 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: Isoform Short of Probable global transcription activator SNF2L2

B: von Hippel-Lindau disease tumor suppressor

C: Elongin-C

D: Elongin-B

E: Isoform Short of Probable global transcription activator SNF2L2

F: von Hippel-Lindau disease tumor suppressor

G: Elongin-C

H: Elongin-B

I: Isoform Short of Probable global transcription activator SNF2L2

J: von Hippel-Lindau disease tumor suppressor

K: Elongin-C

L: Elongin-B

M: Isoform Short of Probable global transcription activator SNF2L2

N: von Hippel-Lindau disease tumor suppressor

O: Elongin-C

P: Elongin-B

Q: Isoform Short of Probable global transcription activator SNF2L2

R: von Hippel-Lindau disease tumor suppressor

S: Elongin-C

T: Elongin-B

U: Isoform Short of Probable global transcription activator SNF2L2

V: von Hippel-Lindau disease tumor suppressor

W: Elongin-C

X: Elongin-B

Y: Isoform Short of Probable global transcription activator SNF2L2

Z: von Hippel-Lindau disease tumor suppressor

a: Elongin-C

b: Elongin-B

c: Isoform Short of Probable global transcription activator SNF2L2

d: von Hippel-Lindau disease tumor suppressor

e: Elongin-C

f: Elongin-B

g: Isoform Short of Probable global transcription activator SNF2L2

h: von Hippel-Lindau disease tumor suppressor

i: Elongin-C

j: Elongin-B

k: Isoform Short of Probable global transcription activator SNF2L2

l: von Hippel-Lindau disease tumor suppressor

m: Elongin-C

n: Elongin-B

hetero molecules

Summary:

• 562 kDa, 40 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	561,912	56
Polymers	551,982	40
Non-polymers	9,931	16
Water	1,369	76

1

Summary:

• Idetical with deposited unit
• defined by author
• Evidence: gel filtration

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	183.960, 203.630, 206.950
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P21212

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	E
1	2	A
2	2	I
1	3	A
2	3	M
1	4	A
2	4	U
1	5	A
2	5	Y
1	6	A
2	6	c
1	7	A
2	7	g
1	8	A
2	8	k
1	9	B
2	9	F
1	10	B
2	10	J
1	11	B
2	11	N
1	12	B
2	12	R
1	13	B
2	13	V
1	14	B
2	14	Z
1	15	B
2	15	d
1	16	B
2	16	h
1	17	B
2	17	l
1	18	C
2	18	G
1	19	C
2	19	K
1	20	C
2	20	O
1	21	C
2	21	S
1	22	C
2	22	W
1	23	C
2	23	a
1	24	C
2	24	e
1	25	C
2	25	i
1	26	C
2	26	m
1	27	D
2	27	H
1	28	D
2	28	L
1	29	D
2	29	P
1	30	D
2	30	T
1	31	D
2	31	X
1	32	D
2	32	b
1	33	D
2	33	f
1	34	D
2	34	j
1	35	D
2	35	n
1	36	E
2	36	I
1	37	E
2	37	M
1	38	E
2	38	Q
1	39	E
2	39	U
1	40	E
2	40	Y
1	41	E
2	41	c
1	42	E
2	42	g
1	43	E
2	43	k
1	44	F
2	44	J
1	45	F
2	45	N
1	46	F
2	46	R
1	47	F
2	47	V
1	48	F
2	48	Z
1	49	F
2	49	d
1	50	F
2	50	h
1	51	F
2	51	l
1	52	G
2	52	K
1	53	G
2	53	O
1	54	G
2	54	S
1	55	G
2	55	W
1	56	G
2	56	a
1	57	G
2	57	e
1	58	G
2	58	i
1	59	G
2	59	m
1	60	H
2	60	L
1	61	H
2	61	P
1	62	H
2	62	T
1	63	H
2	63	X
1	64	H
2	64	b
1	65	H
2	65	f
1	66	H
2	66	j
1	67	H
2	67	n
1	68	I
2	68	M
1	69	I
2	69	Q
1	70	I
2	70	U
1	71	I
2	71	Y
1	72	I
2	72	c
1	73	I
2	73	g
1	74	I
2	74	k
1	75	J
2	75	N
1	76	J
2	76	R
1	77	J
2	77	V
1	78	J
2	78	Z
1	79	J
2	79	d
1	80	J
2	80	h
1	81	J
2	81	l
1	82	K
2	82	O
1	83	K
2	83	S
1	84	K
2	84	W
1	85	K
2	85	a
1	86	K
2	86	e
1	87	K
2	87	i
1	88	K
2	88	m
1	89	L
2	89	P
1	90	L
2	90	T
1	91	L
2	91	X
1	92	L
2	92	b
1	93	L
2	93	f
1	94	L
2	94	j
1	95	L
2	95	n
1	96	M
2	96	U
1	97	M
2	97	Y
1	98	M
2	98	c
1	99	M
2	99	g
1	100	M
2	100	k
1	101	N
2	101	R
1	102	N
2	102	V
1	103	N
2	103	Z
1	104	N
2	104	d
1	105	N
2	105	h
1	106	N
2	106	l
1	107	O
2	107	S
1	108	O
2	108	W
1	109	O
2	109	a
1	110	O
2	110	e
1	111	O
2	111	i
1	112	O
2	112	m
1	113	P
2	113	T
1	114	P
2	114	X
1	115	P
2	115	b
1	116	P
2	116	f
1	117	P
2	117	j
1	118	P
2	118	n
1	119	R
2	119	V
1	120	R
2	120	Z
1	121	R
2	121	d
1	122	R
2	122	h
1	123	R
2	123	l
1	124	S
2	124	W
1	125	S
2	125	a
1	126	S
2	126	e
1	127	S
2	127	i
1	128	S
2	128	m
1	129	T
2	129	X
1	130	T
2	130	b
1	131	T
2	131	f
1	132	T
2	132	j
1	133	T
2	133	n
1	134	U
2	134	Y
1	135	U
2	135	c
1	136	U
2	136	g
1	137	U
2	137	k
1	138	V
2	138	Z
1	139	V
2	139	d
1	140	V
2	140	h
1	141	V
2	141	l
1	142	W
2	142	a
1	143	W
2	143	e
1	144	W
2	144	i
1	145	W
2	145	m
1	146	X
2	146	b
1	147	X
2	147	f
1	148	X
2	148	j
1	149	X
2	149	n
1	150	Y
2	150	c
1	151	Y
2	151	g
1	152	Y
2	152	k
1	153	Z
2	153	d
1	154	Z
2	154	h
1	155	Z
2	155	l
1	156	a
2	156	e
1	157	a
2	157	i
1	158	a
2	158	m
1	159	b
2	159	f
1	160	b
2	160	j
1	161	b
2	161	n
1	162	c
2	162	g
1	163	c
2	163	k
1	164	d
2	164	h
1	165	d
2	165	l
1	166	e
2	166	i
1	167	e
2	167	m
1	168	f
2	168	j
1	169	f
2	169	n
1	170	g
2	170	k
1	171	h
2	171	l
1	172	i
2	172	m
1	173	j
2	173	n

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	1	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
1	2	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	2	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
1	3	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	3	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
1	4	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	4	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
1	5	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	5	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
1	6	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	6	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	7	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	7	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	8	LEU	LEU	GLU	GLU	A	A	12 - 120	12 - 120
2	8	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	9	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	9	VAL	VAL	HIS	HIS	F	F	10 - 156	10 - 156
1	10	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	10	VAL	VAL	HIS	HIS	J	J	10 - 156	10 - 156
1	11	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	11	VAL	VAL	HIS	HIS	N	N	10 - 156	10 - 156
1	12	VAL	VAL	GLN	GLN	B	B	10 - 157	10 - 157
2	12	VAL	VAL	GLN	GLN	R	R	10 - 157	10 - 157
1	13	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	13	VAL	VAL	HIS	HIS	V	V	10 - 156	10 - 156
1	14	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	14	VAL	VAL	HIS	HIS	Z	Z	10 - 156	10 - 156
1	15	VAL	VAL	GLN	GLN	B	B	10 - 157	10 - 157
2	15	VAL	VAL	GLN	GLN	d	DA	10 - 157	10 - 157
1	16	VAL	VAL	HIS	HIS	B	B	10 - 156	10 - 156
2	16	VAL	VAL	HIS	HIS	h	HA	10 - 156	10 - 156
1	17	VAL	VAL	ARG	ARG	B	B	10 - 153	10 - 153
2	17	VAL	VAL	ARG	ARG	l	LA	10 - 153	10 - 153
1	18	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	18	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
1	19	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	19	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
1	20	TYR	TYR	CYS	CYS	C	C	2 - 96	2 - 96
2	20	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
1	21	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	21	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
1	22	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	22	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
1	23	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	23	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
1	24	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	24	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	25	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	25	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	26	MET	MET	CYS	CYS	C	C	1 - 96	1 - 96
2	26	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	27	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	27	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
1	28	ASP	ASP	MET	MET	D	D	2 - 103	2 - 103
2	28	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
1	29	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	29	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
1	30	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	30	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
1	31	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	31	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
1	32	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	32	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
1	33	MET	MET	VAL	VAL	D	D	1 - 102	1 - 102
2	33	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	34	ASP	ASP	MET	MET	D	D	2 - 103	2 - 103
2	34	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	35	MET	MET	LYS	LYS	D	D	1 - 104	1 - 104
2	35	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	36	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	36	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
1	37	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	37	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
1	38	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	38	LEU	LEU	GLU	GLU	Q	Q	12 - 120	12 - 120
1	39	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	39	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
1	40	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	40	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
1	41	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	41	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	42	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	42	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	43	LEU	LEU	GLU	GLU	E	E	12 - 120	12 - 120
2	43	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	44	PRO	PRO	HIS	HIS	F	F	9 - 156	9 - 156
2	44	PRO	PRO	HIS	HIS	J	J	9 - 156	9 - 156
1	45	PRO	PRO	GLN	GLN	F	F	9 - 157	9 - 157
2	45	PRO	PRO	GLN	GLN	N	N	9 - 157	9 - 157
1	46	VAL	VAL	HIS	HIS	F	F	10 - 156	10 - 156
2	46	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
1	47	PRO	PRO	HIS	HIS	F	F	9 - 156	9 - 156
2	47	PRO	PRO	HIS	HIS	V	V	9 - 156	9 - 156
1	48	PRO	PRO	GLN	GLN	F	F	9 - 157	9 - 157
2	48	PRO	PRO	GLN	GLN	Z	Z	9 - 157	9 - 157
1	49	VAL	VAL	HIS	HIS	F	F	10 - 156	10 - 156
2	49	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
1	50	PRO	PRO	HIS	HIS	F	F	9 - 156	9 - 156
2	50	PRO	PRO	HIS	HIS	h	HA	9 - 156	9 - 156
1	51	PRO	PRO	ARG	ARG	F	F	9 - 153	9 - 153
2	51	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	52	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	52	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
1	53	TYR	TYR	CYS	CYS	G	G	2 - 96	2 - 96
2	53	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
1	54	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	54	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
1	55	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	55	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
1	56	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	56	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
1	57	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	57	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	58	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	58	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	59	MET	MET	CYS	CYS	G	G	1 - 96	1 - 96
2	59	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	60	ASP	ASP	MET	MET	H	H	2 - 103	2 - 103
2	60	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
1	61	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
2	61	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
1	62	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
2	62	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
1	63	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
2	63	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
1	64	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
2	64	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
1	65	MET	MET	VAL	VAL	H	H	1 - 102	1 - 102
2	65	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	66	ASP	ASP	MET	MET	H	H	2 - 103	2 - 103
2	66	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	67	MET	MET	LYS	LYS	H	H	1 - 104	1 - 104
2	67	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	68	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	68	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
1	69	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	69	LEU	LEU	GLU	GLU	Q	Q	12 - 120	12 - 120
1	70	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	70	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
1	71	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	71	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
1	72	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	72	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	73	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	73	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	74	LEU	LEU	GLU	GLU	I	I	12 - 120	12 - 120
2	74	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	75	PRO	PRO	HIS	HIS	J	J	9 - 156	9 - 156
2	75	PRO	PRO	HIS	HIS	N	N	9 - 156	9 - 156
1	76	VAL	VAL	HIS	HIS	J	J	10 - 156	10 - 156
2	76	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
1	77	PRO	PRO	GLN	GLN	J	J	9 - 157	9 - 157
2	77	PRO	PRO	GLN	GLN	V	V	9 - 157	9 - 157
1	78	PRO	PRO	HIS	HIS	J	J	9 - 156	9 - 156
2	78	PRO	PRO	HIS	HIS	Z	Z	9 - 156	9 - 156
1	79	VAL	VAL	HIS	HIS	J	J	10 - 156	10 - 156
2	79	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
1	80	PRO	PRO	GLN	GLN	J	J	9 - 157	9 - 157
2	80	PRO	PRO	GLN	GLN	h	HA	9 - 157	9 - 157
1	81	PRO	PRO	ARG	ARG	J	J	9 - 153	9 - 153
2	81	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	82	TYR	TYR	CYS	CYS	K	K	2 - 96	2 - 96
2	82	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
1	83	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	83	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
1	84	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	84	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
1	85	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	85	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
1	86	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	86	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	87	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	87	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	88	MET	MET	CYS	CYS	K	K	1 - 96	1 - 96
2	88	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	89	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
2	89	ASP	ASP	MET	MET	P	P	2 - 103	2 - 103
1	90	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
2	90	ASP	ASP	MET	MET	T	T	2 - 103	2 - 103
1	91	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
2	91	ASP	ASP	MET	MET	X	X	2 - 103	2 - 103
1	92	ASP	ASP	MET	MET	L	L	2 - 103	2 - 103
2	92	ASP	ASP	MET	MET	b	BA	2 - 103	2 - 103
1	93	ASP	ASP	VAL	VAL	L	L	2 - 102	2 - 102
2	93	ASP	ASP	VAL	VAL	f	FA	2 - 102	2 - 102
1	94	ASP	ASP	LYS	LYS	L	L	2 - 104	2 - 104
2	94	ASP	ASP	LYS	LYS	j	JA	2 - 104	2 - 104
1	95	ASP	ASP	LYS	LYS	L	L	2 - 104	2 - 104
2	95	ASP	ASP	LYS	LYS	n	NA	2 - 104	2 - 104
1	96	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
2	96	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
1	97	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
2	97	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
1	98	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
2	98	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	99	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
2	99	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	100	LEU	LEU	GLU	GLU	M	M	12 - 120	12 - 120
2	100	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	101	VAL	VAL	HIS	HIS	N	N	10 - 156	10 - 156
2	101	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
1	102	PRO	PRO	HIS	HIS	N	N	9 - 156	9 - 156
2	102	PRO	PRO	HIS	HIS	V	V	9 - 156	9 - 156
1	103	PRO	PRO	ARG	ARG	N	N	9 - 158	9 - 158
2	103	PRO	PRO	ARG	ARG	Z	Z	9 - 158	9 - 158
1	104	VAL	VAL	HIS	HIS	N	N	10 - 156	10 - 156
2	104	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
1	105	PRO	PRO	HIS	HIS	N	N	9 - 156	9 - 156
2	105	PRO	PRO	HIS	HIS	h	HA	9 - 156	9 - 156
1	106	PRO	PRO	ARG	ARG	N	N	9 - 153	9 - 153
2	106	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	107	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	107	TYR	TYR	CYS	CYS	S	S	2 - 96	2 - 96
1	108	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	108	TYR	TYR	CYS	CYS	W	W	2 - 96	2 - 96
1	109	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	109	TYR	TYR	CYS	CYS	a	AA	2 - 96	2 - 96
1	110	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	110	TYR	TYR	CYS	CYS	e	EA	2 - 96	2 - 96
1	111	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	111	TYR	TYR	CYS	CYS	i	IA	2 - 96	2 - 96
1	112	TYR	TYR	CYS	CYS	O	O	2 - 96	2 - 96
2	112	TYR	TYR	CYS	CYS	m	MA	2 - 96	2 - 96
1	113	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
2	113	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
1	114	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
2	114	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
1	115	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
2	115	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
1	116	MET	MET	VAL	VAL	P	P	1 - 102	1 - 102
2	116	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	117	ASP	ASP	MET	MET	P	P	2 - 103	2 - 103
2	117	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	118	MET	MET	LYS	LYS	P	P	1 - 104	1 - 104
2	118	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	119	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
2	119	VAL	VAL	HIS	HIS	V	V	10 - 156	10 - 156
1	120	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
2	120	VAL	VAL	HIS	HIS	Z	Z	10 - 156	10 - 156
1	121	VAL	VAL	GLN	GLN	R	R	10 - 157	10 - 157
2	121	VAL	VAL	GLN	GLN	d	DA	10 - 157	10 - 157
1	122	VAL	VAL	HIS	HIS	R	R	10 - 156	10 - 156
2	122	VAL	VAL	HIS	HIS	h	HA	10 - 156	10 - 156
1	123	VAL	VAL	ARG	ARG	R	R	10 - 153	10 - 153
2	123	VAL	VAL	ARG	ARG	l	LA	10 - 153	10 - 153
1	124	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
2	124	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
1	125	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
2	125	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
1	126	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
2	126	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	127	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
2	127	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	128	MET	MET	CYS	CYS	S	S	1 - 96	1 - 96
2	128	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	129	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
2	129	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
1	130	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
2	130	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
1	131	MET	MET	VAL	VAL	T	T	1 - 102	1 - 102
2	131	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	132	ASP	ASP	MET	MET	T	T	2 - 103	2 - 103
2	132	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	133	MET	MET	LYS	LYS	T	T	1 - 104	1 - 104
2	133	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	134	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
2	134	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
1	135	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
2	135	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	136	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
2	136	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	137	LEU	LEU	GLU	GLU	U	U	12 - 120	12 - 120
2	137	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	138	PRO	PRO	HIS	HIS	V	V	9 - 156	9 - 156
2	138	PRO	PRO	HIS	HIS	Z	Z	9 - 156	9 - 156
1	139	VAL	VAL	HIS	HIS	V	V	10 - 156	10 - 156
2	139	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
1	140	PRO	PRO	GLN	GLN	V	V	9 - 157	9 - 157
2	140	PRO	PRO	GLN	GLN	h	HA	9 - 157	9 - 157
1	141	PRO	PRO	ARG	ARG	V	V	9 - 153	9 - 153
2	141	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	142	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
2	142	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
1	143	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
2	143	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	144	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
2	144	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	145	MET	MET	CYS	CYS	W	W	1 - 96	1 - 96
2	145	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	146	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
2	146	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
1	147	MET	MET	VAL	VAL	X	X	1 - 102	1 - 102
2	147	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	148	ASP	ASP	MET	MET	X	X	2 - 103	2 - 103
2	148	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	149	MET	MET	LYS	LYS	X	X	1 - 104	1 - 104
2	149	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	150	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
2	150	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
1	151	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
2	151	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	152	LEU	LEU	GLU	GLU	Y	Y	12 - 120	12 - 120
2	152	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	153	VAL	VAL	HIS	HIS	Z	Z	10 - 156	10 - 156
2	153	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
1	154	PRO	PRO	HIS	HIS	Z	Z	9 - 156	9 - 156
2	154	PRO	PRO	HIS	HIS	h	HA	9 - 156	9 - 156
1	155	PRO	PRO	ARG	ARG	Z	Z	9 - 153	9 - 153
2	155	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	156	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
2	156	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
1	157	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
2	157	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	158	MET	MET	CYS	CYS	a	AA	1 - 96	1 - 96
2	158	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	159	MET	MET	VAL	VAL	b	BA	1 - 102	1 - 102
2	159	MET	MET	VAL	VAL	f	FA	1 - 102	1 - 102
1	160	ASP	ASP	MET	MET	b	BA	2 - 103	2 - 103
2	160	ASP	ASP	MET	MET	j	JA	2 - 103	2 - 103
1	161	MET	MET	LYS	LYS	b	BA	1 - 104	1 - 104
2	161	MET	MET	LYS	LYS	n	NA	1 - 104	1 - 104
1	162	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
2	162	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
1	163	LEU	LEU	GLU	GLU	c	CA	12 - 120	12 - 120
2	163	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	164	VAL	VAL	HIS	HIS	d	DA	10 - 156	10 - 156
2	164	VAL	VAL	HIS	HIS	h	HA	10 - 156	10 - 156
1	165	VAL	VAL	ARG	ARG	d	DA	10 - 153	10 - 153
2	165	VAL	VAL	ARG	ARG	l	LA	10 - 153	10 - 153
1	166	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
2	166	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
1	167	MET	MET	CYS	CYS	e	EA	1 - 96	1 - 96
2	167	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	168	ASP	ASP	VAL	VAL	f	FA	2 - 102	2 - 102
2	168	ASP	ASP	VAL	VAL	j	JA	2 - 102	2 - 102
1	169	MET	MET	MET	MET	f	FA	1 - 103	1 - 103
2	169	MET	MET	MET	MET	n	NA	1 - 103	1 - 103
1	170	LEU	LEU	GLU	GLU	g	GA	12 - 120	12 - 120
2	170	LEU	LEU	GLU	GLU	k	KA	12 - 120	12 - 120
1	171	PRO	PRO	ARG	ARG	h	HA	9 - 153	9 - 153
2	171	PRO	PRO	ARG	ARG	l	LA	9 - 153	9 - 153
1	172	MET	MET	CYS	CYS	i	IA	1 - 96	1 - 96
2	172	MET	MET	CYS	CYS	m	MA	1 - 96	1 - 96
1	173	ASP	ASP	LYS	LYS	j	JA	2 - 104	2 - 104
2	173	ASP	ASP	LYS	LYS	n	NA	2 - 104	2 - 104

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173

Components

Protein , 4 types, 40 molecules A E I M Q U Y c g k B F J N R V Z d h l C G K O S W a e i m ...

#1: Protein

A E I M Q U Y c g k
Isoform Short of Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2

Details:

Mass: 13991.118 Da / Num. of mol.: 10 / Fragment: UNP residues 1373-1491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

#2: Protein

B F J N R V Z d h l
von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL

Details:

Mass: 18615.215 Da / Num. of mol.: 10 / Fragment: UNP residues 54-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40337

#3: Protein

C G K O S W a e i m
Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1

Details:

Mass: 10843.420 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15369

#4: Protein

D H L P T X b f j n
Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2

Details:

Mass: 11748.406 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q15370

Non-polymers , 4 types, 92 molecules

#5: Chemical

B-201 F-201 J-201 N-201 R-201 V-201 Z-201 d-201 h-201 k-201
ChemComp-A1BB4 / (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide

Details:

Mass: 891.092 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₄₇H₅₈N₁₀O₆S

#6: Chemical

C-101 S-101 W-101 a-101 e-101
ChemComp-CIT / CITRIC ACID

Details:

Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₆H₈O₇

#7: Chemical

F-202 ChemComp-ACT / ACETATE ION

Details:

Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂

#8: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: N
• Has protein modification: N

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 3.51 ų/Da / Density % sol: 64.97 %
• Crystal grow: Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.26 ; Details: 2% v/v Tacsimate, pH 5.0, 0.1 M tri-sodium citrate, pH 5.26, 11.36% w/v PEG3350, 0.1 M barium chloride dihydrate

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.99999 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2024
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.99999 Å / Relative weight: 1
• Reflection: Resolution: 3.187→49.48 Å / Num. obs: 106916 / % possible obs: 96.8 % / Redundancy: 22.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.355 / R_pim(I) all: 0.077 / R_rim(I) all: 0.363 / Net I/σ(I): 11.9
• Reflection shell: Resolution: 3.187→3.329 Å / Redundancy: 20.9 % / R_merge(I) obs: 1.338 / Num. unique obs: 5346 / CC_1/2: 0.868 / R_pim(I) all: 0.3 / R_rim(I) all: 1.372 / % possible all: 96.6

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.28	data extraction
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.19→49.48 Å / Cor.coef. F_o:F_c: 0.869 / Cor.coef. F_o:F_c free: 0.855 / SU B: 27.156 / SU ML: 0.458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.595 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2848	5456	5.1 %	RANDOM
Rwork	0.2559	-	-	-
obs	0.2574	101460	82.28 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 375.08 Ų / B_iso mean: 80.98 Ų / B_iso min: 0.5 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.66 Å2	-0 Å2	-0 Å2
2-	-	-0.02 Å2	0 Å2
3-	-	-	0.68 Å2

Refinement step

Cycle: final / Resolution: 3.19→49.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	36152	0	709	76	36937
Biso mean	-	-	77.24	21.23	-
Num. residues	-	-	-	-	4465

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	37683
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	36273
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.682	51033
X-RAY DIFFRACTION	r_angle_other_deg	1.232	1.603	83683
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.238	5	4410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.589	21.509	2088
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.422	15	6702
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.285	15	322
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	4887
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	41398
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	8550
X-RAY DIFFRACTION	r_mcbond_it	3.817	8.654	17809
X-RAY DIFFRACTION	r_mcbond_other	3.817	8.654	17807
X-RAY DIFFRACTION	r_mcangle_it	6.62	12.959	22162

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	2754	0.16
1	2	E	2754	0.16
2	1	A	2861	0.18
2	2	I	2861	0.18
3	1	A	3342	0.14
3	2	M	3342	0.14
4	1	A	3285	0.15
4	2	U	3285	0.15
5	1	A	3320	0.13
5	2	Y	3320	0.13
6	1	A	3287	0.16
6	2	c	3287	0.16
7	1	A	3261	0.15
7	2	g	3261	0.15
8	1	A	3264	0.15
8	2	k	3264	0.15
9	1	B	4502	0.13
9	2	F	4502	0.13
10	1	B	4498	0.14
10	2	J	4498	0.14
11	1	B	4448	0.14
11	2	N	4448	0.14
12	1	B	4501	0.14
12	2	R	4501	0.14
13	1	B	4512	0.12
13	2	V	4512	0.12
14	1	B	4504	0.13
14	2	Z	4504	0.13
15	1	B	4491	0.14
15	2	d	4491	0.14
16	1	B	4376	0.14
16	2	h	4376	0.14
17	1	B	4344	0.14
17	2	l	4344	0.14
18	1	C	2520	0.16
18	2	G	2520	0.16
19	1	C	2555	0.15
19	2	K	2555	0.15
20	1	C	2496	0.14
20	2	O	2496	0.14
21	1	C	2476	0.18
21	2	S	2476	0.18
22	1	C	2542	0.13
22	2	W	2542	0.13
23	1	C	2541	0.14
23	2	a	2541	0.14
24	1	C	2517	0.16
24	2	e	2517	0.16
25	1	C	2517	0.15
25	2	i	2517	0.15
26	1	C	2468	0.16
26	2	m	2468	0.16
27	1	D	2722	0.19
27	2	H	2722	0.19
28	1	D	2626	0.2
28	2	L	2626	0.2
29	1	D	2769	0.19
29	2	P	2769	0.19
30	1	D	2708	0.2
30	2	T	2708	0.2
31	1	D	2745	0.18
31	2	X	2745	0.18
32	1	D	2711	0.2
32	2	b	2711	0.2
33	1	D	2653	0.19
33	2	f	2653	0.19
34	1	D	2423	0.23
34	2	j	2423	0.23
35	1	D	2367	0.27
35	2	n	2367	0.27
36	1	E	2548	0.13
36	2	I	2548	0.13
37	1	E	2824	0.12
37	2	M	2824	0.12
38	1	E	2195	0.14
38	2	Q	2195	0.14
39	1	E	2811	0.11
39	2	U	2811	0.11
40	1	E	2814	0.11
40	2	Y	2814	0.11
41	1	E	2787	0.12
41	2	c	2787	0.12
42	1	E	2750	0.12
42	2	g	2750	0.12
43	1	E	2779	0.12
43	2	k	2779	0.12
44	1	F	4536	0.14
44	2	J	4536	0.14
45	1	F	4538	0.15
45	2	N	4538	0.15
46	1	F	4347	0.16
46	2	R	4347	0.16
47	1	F	4457	0.14
47	2	V	4457	0.14
48	1	F	4486	0.15
48	2	Z	4486	0.15
49	1	F	4444	0.15
49	2	d	4444	0.15
50	1	F	4425	0.15
50	2	h	4425	0.15
51	1	F	4380	0.13
51	2	l	4380	0.13
52	1	G	2585	0.16
52	2	K	2585	0.16
53	1	G	2518	0.15
53	2	O	2518	0.15
54	1	G	2483	0.18
54	2	S	2483	0.18
55	1	G	2559	0.15
55	2	W	2559	0.15
56	1	G	2577	0.15
56	2	a	2577	0.15
57	1	G	2618	0.15
57	2	e	2618	0.15
58	1	G	2525	0.16
58	2	i	2525	0.16
59	1	G	2511	0.16
59	2	m	2511	0.16
60	1	H	2733	0.17
60	2	L	2733	0.17
61	1	H	2997	0.13
61	2	P	2997	0.13
62	1	H	2994	0.13
62	2	T	2994	0.13
63	1	H	3025	0.11
63	2	X	3025	0.11
64	1	H	2942	0.13
64	2	b	2942	0.13
65	1	H	2913	0.13
65	2	f	2913	0.13
66	1	H	2413	0.22
66	2	j	2413	0.22
67	1	H	2319	0.26
67	2	n	2319	0.26
68	1	I	2942	0.13
68	2	M	2942	0.13
69	1	I	2443	0.14
69	2	Q	2443	0.14
70	1	I	2951	0.11
70	2	U	2951	0.11
71	1	I	2939	0.13
71	2	Y	2939	0.13
72	1	I	2949	0.14
72	2	c	2949	0.14
73	1	I	2888	0.15
73	2	g	2888	0.15
74	1	I	2935	0.12
74	2	k	2935	0.12
75	1	J	4539	0.15
75	2	N	4539	0.15
76	1	J	4315	0.17
76	2	R	4315	0.17
77	1	J	4502	0.15
77	2	V	4502	0.15
78	1	J	4429	0.15
78	2	Z	4429	0.15
79	1	J	4452	0.15
79	2	d	4452	0.15
80	1	J	4440	0.15
80	2	h	4440	0.15
81	1	J	4370	0.14
81	2	l	4370	0.14
82	1	K	2536	0.15
82	2	O	2536	0.15
83	1	K	2518	0.18
83	2	S	2518	0.18
84	1	K	2550	0.15
84	2	W	2550	0.15
85	1	K	2611	0.14
85	2	a	2611	0.14
86	1	K	2603	0.16
86	2	e	2603	0.16
87	1	K	2535	0.16
87	2	i	2535	0.16
88	1	K	2519	0.16
88	2	m	2519	0.16
89	1	L	2755	0.16
89	2	P	2755	0.16
90	1	L	2716	0.17
90	2	T	2716	0.17
91	1	L	2746	0.16
91	2	X	2746	0.16
92	1	L	2707	0.16
92	2	b	2707	0.16
93	1	L	2706	0.16
93	2	f	2706	0.16
94	1	L	2428	0.23
94	2	j	2428	0.23
95	1	L	2298	0.27
95	2	n	2298	0.27
96	1	M	3387	0.1
96	2	U	3387	0.1
97	1	M	3415	0.07
97	2	Y	3415	0.07
98	1	M	3388	0.1
98	2	c	3388	0.1
99	1	M	3338	0.11
99	2	g	3338	0.11
100	1	M	3379	0.11
100	2	k	3379	0.11
101	1	N	4352	0.17
101	2	R	4352	0.17
102	1	N	4453	0.16
102	2	V	4453	0.16
103	1	N	4433	0.17
103	2	Z	4433	0.17
104	1	N	4438	0.16
104	2	d	4438	0.16
105	1	N	4409	0.16
105	2	h	4409	0.16
106	1	N	4376	0.14
106	2	l	4376	0.14
107	1	O	2553	0.15
107	2	S	2553	0.15
108	1	O	2521	0.13
108	2	W	2521	0.13
109	1	O	2506	0.15
109	2	a	2506	0.15
110	1	O	2513	0.14
110	2	e	2513	0.14
111	1	O	2454	0.17
111	2	i	2454	0.17
112	1	O	2470	0.15
112	2	m	2470	0.15
113	1	P	2989	0.13
113	2	T	2989	0.13
114	1	P	3047	0.11
114	2	X	3047	0.11
115	1	P	2959	0.14
115	2	b	2959	0.14
116	1	P	2973	0.12
116	2	f	2973	0.12
117	1	P	2445	0.22
117	2	j	2445	0.22
118	1	P	2344	0.26
118	2	n	2344	0.26
119	1	R	4449	0.14
119	2	V	4449	0.14
120	1	R	4449	0.14
120	2	Z	4449	0.14
121	1	R	4438	0.15
121	2	d	4438	0.15
122	1	R	4307	0.15
122	2	h	4307	0.15
123	1	R	4280	0.15
123	2	l	4280	0.15
124	1	S	2502	0.16
124	2	W	2502	0.16
125	1	S	2544	0.17
125	2	a	2544	0.17
126	1	S	2524	0.17
126	2	e	2524	0.17
127	1	S	2443	0.19
127	2	i	2443	0.19
128	1	S	2436	0.18
128	2	m	2436	0.18
129	1	T	3084	0.1
129	2	X	3084	0.1
130	1	T	2993	0.13
130	2	b	2993	0.13
131	1	T	2961	0.12
131	2	f	2961	0.12
132	1	T	2426	0.22
132	2	j	2426	0.22
133	1	T	2292	0.26
133	2	n	2292	0.26
134	1	U	3427	0.08
134	2	Y	3427	0.08
135	1	U	3344	0.11
135	2	c	3344	0.11
136	1	U	3317	0.11
136	2	g	3317	0.11
137	1	U	3387	0.1
137	2	k	3387	0.1
138	1	V	4504	0.13
138	2	Z	4504	0.13
139	1	V	4437	0.15
139	2	d	4437	0.15
140	1	V	4456	0.15
140	2	h	4456	0.15
141	1	V	4353	0.14
141	2	l	4353	0.14
142	1	W	2562	0.13
142	2	a	2562	0.13
143	1	W	2564	0.14
143	2	e	2564	0.14
144	1	W	2495	0.16
144	2	i	2495	0.16
145	1	W	2473	0.15
145	2	m	2473	0.15
146	1	X	3016	0.13
146	2	b	3016	0.13
147	1	X	2996	0.11
147	2	f	2996	0.11
148	1	X	2428	0.22
148	2	j	2428	0.22
149	1	X	2329	0.25
149	2	n	2329	0.25
150	1	Y	3360	0.1
150	2	c	3360	0.1
151	1	Y	3324	0.1
151	2	g	3324	0.1
152	1	Y	3380	0.09
152	2	k	3380	0.09
153	1	Z	4479	0.14
153	2	d	4479	0.14
154	1	Z	4361	0.15
154	2	h	4361	0.15
155	1	Z	4318	0.15
155	2	l	4318	0.15
156	1	a	2649	0.13
156	2	e	2649	0.13
157	1	a	2517	0.16
157	2	i	2517	0.16
158	1	a	2483	0.16
158	2	m	2483	0.16
159	1	b	2966	0.12
159	2	f	2966	0.12
160	1	b	2417	0.22
160	2	j	2417	0.22
161	1	b	2297	0.25
161	2	n	2297	0.25
162	1	c	3354	0.11
162	2	g	3354	0.11
163	1	c	3349	0.12
163	2	k	3349	0.12
164	1	d	4358	0.16
164	2	h	4358	0.16
165	1	d	4278	0.16
165	2	l	4278	0.16
166	1	e	2530	0.16
166	2	i	2530	0.16
167	1	e	2516	0.15
167	2	m	2516	0.15
168	1	f	2424	0.22
168	2	j	2424	0.22
169	1	f	2288	0.26
169	2	n	2288	0.26
170	1	g	3318	0.12
170	2	k	3318	0.12
171	1	h	4334	0.13
171	2	l	4334	0.13
172	1	i	2553	0.16
172	2	m	2553	0.16
173	1	j	2318	0.25
173	2	n	2318	0.25

LS refinement shell

Resolution: 3.19→3.269 Å / R_factor R_free error: 0

	Rfactor	Num. reflection	% reflection
Rfree	0.334	153	-
Rwork	0.311	2758	-
obs	-	-	30.72 %