Structure of PDB 1r4n Chain H Binding Site BS02

Receptor Information
>1r4n Chain H (length=418) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGC
ELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFL
NDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISL
LNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQV
NFPMATIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIF
QKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIA
TSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKL
QEVLDYLTNSASLQMKSPAITATNRTLYLQSVTSIEERTRKELGLVDGQE
AVADVTTPQTVLFKLHFT
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain1r4n Chain H Residue 8 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1r4n The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		D79 M80 D81 R90 Q91 K103 K126 I127 Q128 L145 D146
Binding residue
(residue number reindexed from 1)		D68 M69 D70 R79 Q80 K92 K115 I116 Q117 L134 D135
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K21 D146 A216 T217 A219
Catalytic site (residue number reindexed from 1) K10 D135 A205 T206 A208
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1r4n, PDBe:1r4n, PDBj:1r4n
PDBsum1r4n
PubMed14690597
UniProtQ8TBC4|UBA3_HUMAN NEDD8-activating enzyme E1 catalytic subunit (Gene Name=UBA3)

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