Structure of PDB 3gzn Chain B

Receptor sequence
>3gznB (length=429) Species: 9606 (Homo sapiens) [Search protein sequence]
DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGC
ELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFL
NDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISL
LNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQV
NFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIF
QKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIA
TSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKL
QEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKL
KELGLVDGQELAVADVTTPQTVLFKLHFT
3D structure
PDB3gzn Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ.
ChainB
Resolution3.0 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K42 D167 C237 T238 A240
Catalytic site (residue number reindexed from 1) K10 D135 C205 T206 A208
Enzyme Commision number 6.2.1.64: E1 NEDD8-activating enzyme.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN B C223 C364 C367 C191 C332 C335
BS02 B39 B G78 G79 D100 M101 D102 K147 I148 Q149 L166 D167 A171 W174 G46 G47 D68 M69 D70 K115 I116 Q117 L134 D135 A139 W142 PDBbind-CN: -logKd/Ki=8.00,IC50=10nM
BindingDB: IC50=5.0nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3gzn, PDBe:3gzn, PDBj:3gzn
PDBsum3gzn
PubMed20129059
UniProtQ8TBC4|UBA3_HUMAN NEDD8-activating enzyme E1 catalytic subunit (Gene Name=UBA3)

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