4GM3

Crystal structure of human WD repeat domain 5 with compound MM-101

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000123	cellular_component	histone acetyltransferase complex
A	0001501	biological_process	skeletal system development
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0006094	biological_process	gluconeogenesis
A	0006325	biological_process	chromatin organization
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0035097	cellular_component	histone methyltransferase complex
A	0042393	molecular_function	histone binding
A	0042800	molecular_function	histone H3K4 methyltransferase activity
A	0044545	cellular_component	NSL complex
A	0044665	cellular_component	MLL1/2 complex
A	0044666	cellular_component	MLL3/4 complex
A	0045722	biological_process	positive regulation of gluconeogenesis
A	0045815	biological_process	transcription initiation-coupled chromatin remodeling
A	0045893	biological_process	positive regulation of DNA-templated transcription
A	0045995	biological_process	regulation of embryonic development
A	0048188	cellular_component	Set1C/COMPASS complex
A	0051302	biological_process	regulation of cell division
A	0051726	biological_process	regulation of cell cycle
A	0071339	cellular_component	MLL1 complex
A	0072686	cellular_component	mitotic spindle
A	0097228	cellular_component	sperm principal piece
A	0140004	molecular_function	histone H3Q5ser reader activity
A	0140109	molecular_function	histone H3K4me1 reader activity
A	0140672	cellular_component	ATAC complex
B	0000122	biological_process	negative regulation of transcription by RNA polymerase II
B	0000123	cellular_component	histone acetyltransferase complex
B	0001501	biological_process	skeletal system development
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0006094	biological_process	gluconeogenesis
B	0006325	biological_process	chromatin organization
B	0006355	biological_process	regulation of DNA-templated transcription
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0035097	cellular_component	histone methyltransferase complex
B	0042393	molecular_function	histone binding
B	0042800	molecular_function	histone H3K4 methyltransferase activity
B	0044545	cellular_component	NSL complex
B	0044665	cellular_component	MLL1/2 complex
B	0044666	cellular_component	MLL3/4 complex
B	0045722	biological_process	positive regulation of gluconeogenesis
B	0045815	biological_process	transcription initiation-coupled chromatin remodeling
B	0045893	biological_process	positive regulation of DNA-templated transcription
B	0045995	biological_process	regulation of embryonic development
B	0048188	cellular_component	Set1C/COMPASS complex
B	0051302	biological_process	regulation of cell division
B	0051726	biological_process	regulation of cell cycle
B	0071339	cellular_component	MLL1 complex
B	0072686	cellular_component	mitotic spindle
B	0097228	cellular_component	sperm principal piece
B	0140004	molecular_function	histone H3Q5ser reader activity
B	0140109	molecular_function	histone H3K4me1 reader activity
B	0140672	cellular_component	ATAC complex
C	0000122	biological_process	negative regulation of transcription by RNA polymerase II
C	0000123	cellular_component	histone acetyltransferase complex
C	0001501	biological_process	skeletal system development
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0006094	biological_process	gluconeogenesis
C	0006325	biological_process	chromatin organization
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0035097	cellular_component	histone methyltransferase complex
C	0042393	molecular_function	histone binding
C	0042800	molecular_function	histone H3K4 methyltransferase activity
C	0044545	cellular_component	NSL complex
C	0044665	cellular_component	MLL1/2 complex
C	0044666	cellular_component	MLL3/4 complex
C	0045722	biological_process	positive regulation of gluconeogenesis
C	0045815	biological_process	transcription initiation-coupled chromatin remodeling
C	0045893	biological_process	positive regulation of DNA-templated transcription
C	0045995	biological_process	regulation of embryonic development
C	0048188	cellular_component	Set1C/COMPASS complex
C	0051302	biological_process	regulation of cell division
C	0051726	biological_process	regulation of cell cycle
C	0071339	cellular_component	MLL1 complex
C	0072686	cellular_component	mitotic spindle
C	0097228	cellular_component	sperm principal piece
C	0140004	molecular_function	histone H3Q5ser reader activity
C	0140109	molecular_function	histone H3K4me1 reader activity
C	0140672	cellular_component	ATAC complex
D	0000122	biological_process	negative regulation of transcription by RNA polymerase II
D	0000123	cellular_component	histone acetyltransferase complex
D	0001501	biological_process	skeletal system development
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0006094	biological_process	gluconeogenesis
D	0006325	biological_process	chromatin organization
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0035097	cellular_component	histone methyltransferase complex
D	0042393	molecular_function	histone binding
D	0042800	molecular_function	histone H3K4 methyltransferase activity
D	0044545	cellular_component	NSL complex
D	0044665	cellular_component	MLL1/2 complex
D	0044666	cellular_component	MLL3/4 complex
D	0045722	biological_process	positive regulation of gluconeogenesis
D	0045815	biological_process	transcription initiation-coupled chromatin remodeling
D	0045893	biological_process	positive regulation of DNA-templated transcription
D	0045995	biological_process	regulation of embryonic development
D	0048188	cellular_component	Set1C/COMPASS complex
D	0051302	biological_process	regulation of cell division
D	0051726	biological_process	regulation of cell cycle
D	0071339	cellular_component	MLL1 complex
D	0072686	cellular_component	mitotic spindle
D	0097228	cellular_component	sperm principal piece
D	0140004	molecular_function	histone H3Q5ser reader activity
D	0140109	molecular_function	histone H3K4me1 reader activity
D	0140672	cellular_component	ATAC complex
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000123	cellular_component	histone acetyltransferase complex
E	0001501	biological_process	skeletal system development
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0006094	biological_process	gluconeogenesis
E	0006325	biological_process	chromatin organization
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0035097	cellular_component	histone methyltransferase complex
E	0042393	molecular_function	histone binding
E	0042800	molecular_function	histone H3K4 methyltransferase activity
E	0044545	cellular_component	NSL complex
E	0044665	cellular_component	MLL1/2 complex
E	0044666	cellular_component	MLL3/4 complex
E	0045722	biological_process	positive regulation of gluconeogenesis
E	0045815	biological_process	transcription initiation-coupled chromatin remodeling
E	0045893	biological_process	positive regulation of DNA-templated transcription
E	0045995	biological_process	regulation of embryonic development
E	0048188	cellular_component	Set1C/COMPASS complex
E	0051302	biological_process	regulation of cell division
E	0051726	biological_process	regulation of cell cycle
E	0071339	cellular_component	MLL1 complex
E	0072686	cellular_component	mitotic spindle
E	0097228	cellular_component	sperm principal piece
E	0140004	molecular_function	histone H3Q5ser reader activity
E	0140109	molecular_function	histone H3K4me1 reader activity
E	0140672	cellular_component	ATAC complex
F	0000122	biological_process	negative regulation of transcription by RNA polymerase II
F	0000123	cellular_component	histone acetyltransferase complex
F	0001501	biological_process	skeletal system development
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0006094	biological_process	gluconeogenesis
F	0006325	biological_process	chromatin organization
F	0006355	biological_process	regulation of DNA-templated transcription
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0035097	cellular_component	histone methyltransferase complex
F	0042393	molecular_function	histone binding
F	0042800	molecular_function	histone H3K4 methyltransferase activity
F	0044545	cellular_component	NSL complex
F	0044665	cellular_component	MLL1/2 complex
F	0044666	cellular_component	MLL3/4 complex
F	0045722	biological_process	positive regulation of gluconeogenesis
F	0045815	biological_process	transcription initiation-coupled chromatin remodeling
F	0045893	biological_process	positive regulation of DNA-templated transcription
F	0045995	biological_process	regulation of embryonic development
F	0048188	cellular_component	Set1C/COMPASS complex
F	0051302	biological_process	regulation of cell division
F	0051726	biological_process	regulation of cell cycle
F	0071339	cellular_component	MLL1 complex
F	0072686	cellular_component	mitotic spindle
F	0097228	cellular_component	sperm principal piece
F	0140004	molecular_function	histone H3Q5ser reader activity
F	0140109	molecular_function	histone H3K4me1 reader activity
F	0140672	cellular_component	ATAC complex
G	0000122	biological_process	negative regulation of transcription by RNA polymerase II
G	0000123	cellular_component	histone acetyltransferase complex
G	0001501	biological_process	skeletal system development
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0006094	biological_process	gluconeogenesis
G	0006325	biological_process	chromatin organization
G	0006355	biological_process	regulation of DNA-templated transcription
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0035097	cellular_component	histone methyltransferase complex
G	0042393	molecular_function	histone binding
G	0042800	molecular_function	histone H3K4 methyltransferase activity
G	0044545	cellular_component	NSL complex
G	0044665	cellular_component	MLL1/2 complex
G	0044666	cellular_component	MLL3/4 complex
G	0045722	biological_process	positive regulation of gluconeogenesis
G	0045815	biological_process	transcription initiation-coupled chromatin remodeling
G	0045893	biological_process	positive regulation of DNA-templated transcription
G	0045995	biological_process	regulation of embryonic development
G	0048188	cellular_component	Set1C/COMPASS complex
G	0051302	biological_process	regulation of cell division
G	0051726	biological_process	regulation of cell cycle
G	0071339	cellular_component	MLL1 complex
G	0072686	cellular_component	mitotic spindle
G	0097228	cellular_component	sperm principal piece
G	0140004	molecular_function	histone H3Q5ser reader activity
G	0140109	molecular_function	histone H3K4me1 reader activity
G	0140672	cellular_component	ATAC complex
H	0000122	biological_process	negative regulation of transcription by RNA polymerase II
H	0000123	cellular_component	histone acetyltransferase complex
H	0001501	biological_process	skeletal system development
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0006094	biological_process	gluconeogenesis
H	0006325	biological_process	chromatin organization
H	0006355	biological_process	regulation of DNA-templated transcription
H	0006357	biological_process	regulation of transcription by RNA polymerase II
H	0035097	cellular_component	histone methyltransferase complex
H	0042393	molecular_function	histone binding
H	0042800	molecular_function	histone H3K4 methyltransferase activity
H	0044545	cellular_component	NSL complex
H	0044665	cellular_component	MLL1/2 complex
H	0044666	cellular_component	MLL3/4 complex
H	0045722	biological_process	positive regulation of gluconeogenesis
H	0045815	biological_process	transcription initiation-coupled chromatin remodeling
H	0045893	biological_process	positive regulation of DNA-templated transcription
H	0045995	biological_process	regulation of embryonic development
H	0048188	cellular_component	Set1C/COMPASS complex
H	0051302	biological_process	regulation of cell division
H	0051726	biological_process	regulation of cell cycle
H	0071339	cellular_component	MLL1 complex
H	0072686	cellular_component	mitotic spindle
H	0097228	cellular_component	sperm principal piece
H	0140004	molecular_function	histone H3Q5ser reader activity
H	0140109	molecular_function	histone H3K4me1 reader activity
H	0140672	cellular_component	ATAC complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	BINDING SITE FOR CHAIN I OF MM-101

Chain	Residue
A	VAL48
A	LYS259
A	TYR260
A	CYS261
A	PHE263
A	LEU321
L	0XL2
L	0XM5
A	SER49
A	GLY89
A	SER91
A	ASP107
A	TYR131
A	PHE133
A	PHE149
A	SER175

---

site_id	AC2
Number of Residues	16
Details	BINDING SITE FOR CHAIN J OF MM-101

Chain	Residue
B	VAL48
B	SER49
B	ALA65
B	GLY89
B	SER91
B	ASP107
B	TYR131
B	PHE133
B	PHE149
B	SER175
B	LYS259
B	TYR260
B	CYS261
B	PHE263
B	LEU321
K	0XL2

---

site_id	AC3
Number of Residues	16
Details	BINDING SITE FOR CHAIN K OF MM-101

Chain	Residue
C	VAL48
C	ALA65
C	GLY89
C	ILE90
C	SER91
C	ASP107
C	TYR131
C	PHE133
C	PHE149
C	SER175
C	LYS259
C	TYR260
C	CYS261
C	PHE263
C	LEU321
J	0XM5

---

site_id	AC4
Number of Residues	14
Details	BINDING SITE FOR CHAIN L OF MM-101

Chain	Residue
D	ALA65
D	GLY89
D	SER91
D	ASP107
D	TYR131
D	PHE133
D	SER175
D	LYS259
D	TYR260
D	CYS261
D	PHE263
D	LEU321
I	0XL2
I	0XM5

---

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR CHAIN M OF MM-101

Chain	Residue
E	SER49
E	ALA65
E	GLY89
E	SER91
E	ASP107
E	TYR131
E	PHE133
E	SER175
E	LYS259
E	TYR260
E	CYS261
E	PHE263
E	LEU321
P	0XL2
P	0XM5

---

site_id	AC6
Number of Residues	18
Details	BINDING SITE FOR CHAIN N OF MM-101

Chain	Residue
F	VAL48
F	SER49
F	GLY89
F	ILE90
F	SER91
F	ASP107
F	TYR131
F	PHE133
F	PHE149
F	SER175
F	LYS259
F	TYR260
F	CYS261
F	PHE263
F	LEU321
G	TYR131
O	0XL2
O	0XM5

---

site_id	AC7
Number of Residues	16
Details	BINDING SITE FOR CHAIN O OF MM-101

Chain	Residue
G	GLY89
G	SER91
G	ASP107
G	TYR131
G	PHE133
G	SER175
G	TYR260
G	CYS261
G	PHE263
G	LEU321
N	0XL2
N	0XM5
F	TYR131
G	VAL48
G	SER49
G	ALA65

---

site_id	AC8
Number of Residues	16
Details	BINDING SITE FOR CHAIN P OF MM-101

Chain	Residue
H	ALA65
H	GLY89
H	ILE90
H	SER91
H	ASP107
H	TYR131
H	PHE133
H	PHE149
H	SER175
H	LYS259
H	TYR260
H	CYS261
H	PHE263
H	LEU321
M	0XL2
M	0XM5

---

Functional Information from PROSITE/UniProt

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. LVSAsdDkTLKIWDV

Chain	Residue	Details
A	LEU102-VAL116
A	ILE144-VAL158
A	ILE186-THR200
A	ILE274-LEU288

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	312
Details	Repeat: {"description":"WD 1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	328
Details	Repeat: {"description":"WD 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	320
Details	Repeat: {"description":"WD 3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	312
Details	Repeat: {"description":"WD 4"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	328
Details	Repeat: {"description":"WD 5"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	320
Details	Repeat: {"description":"WD 6"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	272
Details	Repeat: {"description":"WD 7"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	32
Details	Site: {"description":"Important for interaction with histone H3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	8
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	16
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---