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6H0F

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0003676molecular_functionnucleic acid binding
A0005634cellular_componentnucleus
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0016020cellular_componentmembrane
B0016567biological_processprotein ubiquitination
B0030177biological_processpositive regulation of Wnt signaling pathway
B0031333biological_processnegative regulation of protein-containing complex assembly
B0031334biological_processpositive regulation of protein-containing complex assembly
B0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
B0034766biological_processnegative regulation of monoatomic ion transmembrane transport
B0035641biological_processlocomotory exploration behavior
B0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
B0044325molecular_functiontransmembrane transporter binding
B0046872molecular_functionmetal ion binding
B0048471cellular_componentperinuclear region of cytoplasm
B0060173biological_processlimb development
D0003676molecular_functionnucleic acid binding
D0005634cellular_componentnucleus
E0005515molecular_functionprotein binding
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0016020cellular_componentmembrane
E0016567biological_processprotein ubiquitination
E0030177biological_processpositive regulation of Wnt signaling pathway
E0031333biological_processnegative regulation of protein-containing complex assembly
E0031334biological_processpositive regulation of protein-containing complex assembly
E0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
E0034766biological_processnegative regulation of monoatomic ion transmembrane transport
E0035641biological_processlocomotory exploration behavior
E0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
E0044325molecular_functiontransmembrane transporter binding
E0046872molecular_functionmetal ion binding
E0048471cellular_componentperinuclear region of cytoplasm
E0060173biological_processlimb development
G0003676molecular_functionnucleic acid binding
G0005634cellular_componentnucleus
H0005515molecular_functionprotein binding
H0005634cellular_componentnucleus
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0016020cellular_componentmembrane
H0016567biological_processprotein ubiquitination
H0030177biological_processpositive regulation of Wnt signaling pathway
H0031333biological_processnegative regulation of protein-containing complex assembly
H0031334biological_processpositive regulation of protein-containing complex assembly
H0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
H0034766biological_processnegative regulation of monoatomic ion transmembrane transport
H0035641biological_processlocomotory exploration behavior
H0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
H0044325molecular_functiontransmembrane transporter binding
H0046872molecular_functionmetal ion binding
H0048471cellular_componentperinuclear region of cytoplasm
H0060173biological_processlimb development
J0003676molecular_functionnucleic acid binding
J0005634cellular_componentnucleus
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005737cellular_componentcytoplasm
K0005829cellular_componentcytosol
K0016020cellular_componentmembrane
K0016567biological_processprotein ubiquitination
K0030177biological_processpositive regulation of Wnt signaling pathway
K0031333biological_processnegative regulation of protein-containing complex assembly
K0031334biological_processpositive regulation of protein-containing complex assembly
K0031464cellular_componentCul4A-RING E3 ubiquitin ligase complex
K0034766biological_processnegative regulation of monoatomic ion transmembrane transport
K0035641biological_processlocomotory exploration behavior
K0043161biological_processproteasome-mediated ubiquitin-dependent protein catabolic process
K0044325molecular_functiontransmembrane transporter binding
K0046872molecular_functionmetal ion binding
K0048471cellular_componentperinuclear region of cytoplasm
K0060173biological_processlimb development
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue ZN B 501
ChainResidue
BCYS323
BCYS326
BCYS391
BCYS394

site_idAC2
Number of Residues15
Detailsbinding site for residue Y70 B 502
ChainResidue
BTRP380
BTRP386
BTRP400
BPHE402
CGLN146
CCYS147
CASN148
CGLN149
CCYS150
CGLY151
BASN351
BPRO352
BHIS353
BGLU377
BHIS378

site_idAC3
Number of Residues4
Detailsbinding site for residue ZN C 201
ChainResidue
CCYS147
CCYS150
CHIS163
CHIS167

site_idAC4
Number of Residues4
Detailsbinding site for residue ZN E 501
ChainResidue
ECYS323
ECYS326
ECYS391
ECYS394

site_idAC5
Number of Residues16
Detailsbinding site for residue Y70 E 502
ChainResidue
EASN351
EPRO352
EHIS353
EGLU377
EHIS378
ETRP380
ETRP386
ETRP400
EPHE402
EHOH602
FGLN146
FCYS147
FASN148
FGLN149
FCYS150
FGLY151

site_idAC6
Number of Residues4
Detailsbinding site for residue ZN F 201
ChainResidue
FCYS147
FCYS150
FHIS163
FHIS167

site_idAC7
Number of Residues4
Detailsbinding site for residue ZN H 501
ChainResidue
HCYS323
HCYS326
HCYS391
HCYS394

site_idAC8
Number of Residues16
Detailsbinding site for residue Y70 H 502
ChainResidue
HASN351
HPRO352
HHIS353
HGLU377
HHIS378
HSER379
HTRP380
HTRP386
HTRP400
HPHE402
IGLN146
ICYS147
IASN148
IGLN149
ICYS150
IGLY151

site_idAC9
Number of Residues4
Detailsbinding site for residue ZN I 201
ChainResidue
ICYS147
ICYS150
IHIS163
IHIS167

site_idAD1
Number of Residues4
Detailsbinding site for residue ZN K 501
ChainResidue
KCYS323
KCYS326
KCYS391
KCYS394

site_idAD2
Number of Residues15
Detailsbinding site for residue Y70 K 502
ChainResidue
KASN351
KPRO352
KHIS353
KGLU377
KHIS378
KTRP380
KTRP386
KTRP400
KPHE402
LGLN146
LCYS147
LASN148
LGLN149
LCYS150
LGLY151

site_idAD3
Number of Residues4
Detailsbinding site for residue ZN L 201
ChainResidue
LCYS147
LCYS150
LHIS163
LHIS167

Functional Information from PROSITE/UniProt
site_idPS00028
Number of Residues21
DetailsZINC_FINGER_C2H2_1 Zinc finger C2H2 type domain signature. Cnq..CgasFtqkgnllrHikl..H
ChainResidueDetails
CCYS147-HIS167

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1372
DetailsRegion: {"description":"WD repeat beta-propeller A"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1002
DetailsRegion: {"description":"WD repeat beta-propeller C"}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues1107
DetailsRegion: {"description":"Interaction with CDT1 and CUL4A","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues4
DetailsModified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues4
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues8
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues952
DetailsDomain: {"description":"Lon N-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU01123","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues432
DetailsDomain: {"description":"CULT","evidences":[{"source":"PROSITE-ProRule","id":"PRU01124","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues28
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25108355","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4TZ4","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues88
DetailsZinc finger: {"description":"C2H2-type 2","evidences":[{"source":"PROSITE-ProRule","id":"PRU00042","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues36
DetailsRegion: {"description":"Required for both high-affinity DNA binding and pericentromeric heterochromatin localization","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues8
DetailsSite: {"description":"Required for both pericentromeric heterochromatin localization and complete DNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues4
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q03267","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

239803

PDB entries from 2025-08-06

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