6H0F

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003676	molecular_function	nucleic acid binding
A	0005634	cellular_component	nucleus
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0016020	cellular_component	membrane
B	0016567	biological_process	protein ubiquitination
B	0030177	biological_process	positive regulation of Wnt signaling pathway
B	0031333	biological_process	negative regulation of protein-containing complex assembly
B	0031334	biological_process	positive regulation of protein-containing complex assembly
B	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
B	0034766	biological_process	negative regulation of monoatomic ion transmembrane transport
B	0035641	biological_process	locomotory exploration behavior
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0044325	molecular_function	transmembrane transporter binding
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0060173	biological_process	limb development
D	0003676	molecular_function	nucleic acid binding
D	0005634	cellular_component	nucleus
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0016020	cellular_component	membrane
E	0016567	biological_process	protein ubiquitination
E	0030177	biological_process	positive regulation of Wnt signaling pathway
E	0031333	biological_process	negative regulation of protein-containing complex assembly
E	0031334	biological_process	positive regulation of protein-containing complex assembly
E	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
E	0034766	biological_process	negative regulation of monoatomic ion transmembrane transport
E	0035641	biological_process	locomotory exploration behavior
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0044325	molecular_function	transmembrane transporter binding
E	0046872	molecular_function	metal ion binding
E	0048471	cellular_component	perinuclear region of cytoplasm
E	0060173	biological_process	limb development
G	0003676	molecular_function	nucleic acid binding
G	0005634	cellular_component	nucleus
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0016020	cellular_component	membrane
H	0016567	biological_process	protein ubiquitination
H	0030177	biological_process	positive regulation of Wnt signaling pathway
H	0031333	biological_process	negative regulation of protein-containing complex assembly
H	0031334	biological_process	positive regulation of protein-containing complex assembly
H	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
H	0034766	biological_process	negative regulation of monoatomic ion transmembrane transport
H	0035641	biological_process	locomotory exploration behavior
H	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
H	0044325	molecular_function	transmembrane transporter binding
H	0046872	molecular_function	metal ion binding
H	0048471	cellular_component	perinuclear region of cytoplasm
H	0060173	biological_process	limb development
J	0003676	molecular_function	nucleic acid binding
J	0005634	cellular_component	nucleus
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0016020	cellular_component	membrane
K	0016567	biological_process	protein ubiquitination
K	0030177	biological_process	positive regulation of Wnt signaling pathway
K	0031333	biological_process	negative regulation of protein-containing complex assembly
K	0031334	biological_process	positive regulation of protein-containing complex assembly
K	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
K	0034766	biological_process	negative regulation of monoatomic ion transmembrane transport
K	0035641	biological_process	locomotory exploration behavior
K	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
K	0044325	molecular_function	transmembrane transporter binding
K	0046872	molecular_function	metal ion binding
K	0048471	cellular_component	perinuclear region of cytoplasm
K	0060173	biological_process	limb development

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN B 501

Chain	Residue
B	CYS323
B	CYS326
B	CYS391
B	CYS394

---

site_id	AC2
Number of Residues	15
Details	binding site for residue Y70 B 502

Chain	Residue
B	TRP380
B	TRP386
B	TRP400
B	PHE402
C	GLN146
C	CYS147
C	ASN148
C	GLN149
C	CYS150
C	GLY151
B	ASN351
B	PRO352
B	HIS353
B	GLU377
B	HIS378

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN C 201

Chain	Residue
C	CYS147
C	CYS150
C	HIS163
C	HIS167

---

site_id	AC4
Number of Residues	4
Details	binding site for residue ZN E 501

Chain	Residue
E	CYS323
E	CYS326
E	CYS391
E	CYS394

---

site_id	AC5
Number of Residues	16
Details	binding site for residue Y70 E 502

Chain	Residue
E	ASN351
E	PRO352
E	HIS353
E	GLU377
E	HIS378
E	TRP380
E	TRP386
E	TRP400
E	PHE402
E	HOH602
F	GLN146
F	CYS147
F	ASN148
F	GLN149
F	CYS150
F	GLY151

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN F 201

Chain	Residue
F	CYS147
F	CYS150
F	HIS163
F	HIS167

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN H 501

Chain	Residue
H	CYS323
H	CYS326
H	CYS391
H	CYS394

---

site_id	AC8
Number of Residues	16
Details	binding site for residue Y70 H 502

Chain	Residue
H	ASN351
H	PRO352
H	HIS353
H	GLU377
H	HIS378
H	SER379
H	TRP380
H	TRP386
H	TRP400
H	PHE402
I	GLN146
I	CYS147
I	ASN148
I	GLN149
I	CYS150
I	GLY151

---

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN I 201

Chain	Residue
I	CYS147
I	CYS150
I	HIS163
I	HIS167

---

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN K 501

Chain	Residue
K	CYS323
K	CYS326
K	CYS391
K	CYS394

---

site_id	AD2
Number of Residues	15
Details	binding site for residue Y70 K 502

Chain	Residue
K	ASN351
K	PRO352
K	HIS353
K	GLU377
K	HIS378
K	TRP380
K	TRP386
K	TRP400
K	PHE402
L	GLN146
L	CYS147
L	ASN148
L	GLN149
L	CYS150
L	GLY151

---

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN L 201

Chain	Residue
L	CYS147
L	CYS150
L	HIS163
L	HIS167

---

Functional Information from PROSITE/UniProt

site_id	PS00028
Number of Residues	21
Details	ZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnq..CgasFtqkgnllrHikl..H

Chain	Residue	Details
C	CYS147-HIS167

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1372
Details	Region: {"description":"WD repeat beta-propeller A"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1002
Details	Region: {"description":"WD repeat beta-propeller C"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1107
Details	Region: {"description":"Interaction with CDT1 and CUL4A","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	8
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

---

site_id	SWS_FT_FI8
Number of Residues	952
Details	Domain: {"description":"Lon N-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU01123","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	432
Details	Domain: {"description":"CULT","evidences":[{"source":"PROSITE-ProRule","id":"PRU01124","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	28
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	88
Details	Zinc finger: {"description":"C2H2-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00042","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	36
Details	Region: {"description":"Required for both high-affinity DNA binding and pericentromeric heterochromatin localization","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	8
Details	Site: {"description":"Required for both pericentromeric heterochromatin localization and complete DNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q03267","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---