Structure of PDB 4r8p Chain L Binding Site BS03

Receptor Information
>4r8p Chain L (length=254) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTT
KECLHRFCADCIITALRSGNKECPTCRKKLVSKRSLRPDPNFDALISKIY
PSGSGSRSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDS
PYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQW
SPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISREWTQ
KYAM
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4r8p Chain L Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r8p Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.
Resolution3.2846 Å
Binding residue
(original residue number in PDB)		C67 H69 C87
Binding residue
(residue number reindexed from 1)		C53 H55 C73
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) C285
Catalytic site (residue number reindexed from 1) C192
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.
2.3.2.27: RING-type E3 ubiquitin transferase.
Gene Ontology
Molecular Function
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0019787 ubiquitin-like protein transferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0061630 ubiquitin protein ligase activity
GO:0061631 ubiquitin conjugating enzyme activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0000209 protein polyubiquitination
GO:0006281 DNA repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006513 protein monoubiquitination
GO:0006915 apoptotic process
GO:0016567 protein ubiquitination
GO:0030514 negative regulation of BMP signaling pathway
GO:0036211 protein modification process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0051865 protein autoubiquitination
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination
GO:0085020 protein K6-linked ubiquitination
GO:1903955 positive regulation of protein targeting to mitochondrion
Cellular Component
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005768 endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0010008 endosome membrane
GO:0070062 extracellular exosome

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Biological Process
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Cellular Component
External links
PDB RCSB:4r8p, PDBe:4r8p, PDBj:4r8p
PDBsum4r8p
PubMed25355358
UniProtP61077|UB2D3_HUMAN Ubiquitin-conjugating enzyme E2 D3 (Gene Name=UBE2D3);
Q99496|RING2_HUMAN E3 ubiquitin-protein ligase RING2 (Gene Name=RNF2)

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