Structure of PDB 3dbl Chain B Binding Site BS01

Receptor Information
>3dbl Chain B (length=432) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLG
CELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEF
LNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLIS
LLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQ
VNFPMATIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWI
FQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKI
ATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAK
LQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSK
TLKELGLVDGQELAVADVTTPQTVLFKLHFTS
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 chain3dbl Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dbl Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		C202 C343 C346
Binding residue
(residue number reindexed from 1)		C192 C333 C336
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K21 D146 A216 T217 A219
Catalytic site (residue number reindexed from 1) K11 D136 A206 T207 A209
Enzyme Commision number 6.2.1.64: E1 NEDD8-activating enzyme.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016874 ligase activity
GO:0019781 NEDD8 activating enzyme activity
GO:0019788 NEDD8 transferase activity
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity
Biological Process
GO:0000278 mitotic cell cycle
GO:0006508 proteolysis
GO:0007113 endomitotic cell cycle
GO:0036211 protein modification process
GO:0043687 post-translational protein modification
GO:0045116 protein neddylation
GO:0051726 regulation of cell cycle
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dbl, PDBe:3dbl, PDBj:3dbl
PDBsum3dbl
PubMed18652489
UniProtQ8TBC4|UBA3_HUMAN NEDD8-activating enzyme E1 catalytic subunit (Gene Name=UBA3)

[Back to BioLiP]