9Q03

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0016020	cellular_component	membrane
C	0016567	biological_process	protein ubiquitination
C	0030177	biological_process	positive regulation of Wnt signaling pathway
C	0031333	biological_process	negative regulation of protein-containing complex assembly
C	0031334	biological_process	positive regulation of protein-containing complex assembly
C	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
C	0034766	biological_process	negative regulation of monoatomic ion transmembrane transport
C	0035641	biological_process	locomotory exploration behavior
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0044325	molecular_function	transmembrane transporter binding
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0060173	biological_process	limb development

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	Neighbourhood of Ion 1:C_ZN_3999 (Entity 4)

Chain	Residue
C	CYS323
C	GLN325
C	CYS326
C	CYS391
C	SER396

---

site_id	AC2
Number of Residues	29
Details	Neighbourhood of 1:C_LIG_4000 (Entity 5)

Chain	Residue
A	GLY55
A	TYR58
A	PHE89
A	GLN113
A	MET114
A	GLU115
A	HIS116
B	HIS14
B	ASP17
B	VAL18
B	ASN21
B	ARG24
B	LEU25
B	ARG28
C	VAL350
C	ASN351
C	PRO352
C	HIS353
C	GLU377
C	HIS378
C	SER379
C	TRP380
C	TRP386
C	TRP400
C	PHE402
A	MET51
A	ALA52
A	CYS53
A	SER54

---

site_id	AC3
Number of Residues	72
Details	Pocket 1 in Model 1 Assembly 1 (Ligand C_LIG_4000 (Entity 5)

Chain	Residue
C	SER396
C	HIS397
C	TRP400
C	PHE402
C	THR418
C	SER420
C	ALA421
A	MET51
A	ALA52
A	CYS53
A	SER54
A	GLY55
A	TYR58
A	SER59
A	THR62
A	PHE89
A	ALA109
A	MET110
A	GLN113
A	MET114
A	GLU115
A	HIS116
A	VAL117
A	VAL118
A	ASP119
A	THR120
A	ARG122
A	LYS123
B	PHE11
B	THR12
B	ARG13
B	HIS14
B	SER16
B	ASP17
B	VAL18
B	LEU20
B	ASN21
B	ARG24
B	LEU25
B	ARG28
B	ILE30
B	ARG94
C	GLN100
C	PHE102
C	HIS103
C	PRO104
C	VAL107
C	ASP149
C	ILE152
C	GLU153
C	ILE154
C	LYS156
C	VAL350
C	ASN351
C	PRO352
C	HIS353
C	TYR355
C	HIS357
C	ILE371
C	GLY372
C	ARG373
C	PRO374
C	SER375
C	GLU377
C	HIS378
C	SER379
C	TRP380
C	TRP386
C	THR387
C	VAL388
C	GLN390
C	ALA395

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	134
Details	Domain: {"description":"BTB","evidences":[{"source":"PROSITE-ProRule","id":"PRU00037","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	108
Details	Domain: {"description":"CULT","evidences":[{"source":"PROSITE-ProRule","id":"PRU01124","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---