Structure of PDB 3vx3 Chain A Binding Site BS01

Receptor Information
>3vx3 Chain A (length=235) Species: 69014 (Thermococcus kodakarensis KOD1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IDPREIAINARLEGVKRIIPVVSGKGGVGKSLVSTTLALVLAEKGYRVGL
LDLDFHGASDHVILGFEPKEFPEEDRGVVPPTVHGIKFMTIAYYTTPLRG
KEISDALIELLTITRWDELDYLVIDMPPGLGDQLLDVLRFLKRGEFLVVA
TPSKLSLNVVRKLIELLKEEGHKVIGVVENMKLREKDVEKLAEEFGVPYL
VGIPFYPDLDAKVGNVEELMKTEFAGKVRELAGRL
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3vx3 Chain A Residue 301 [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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PDB3vx3 Identification and Structure of a Novel Archaeal HypB for [NiFe] Hydrogenase Maturation
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G30 V31 G32 K33 S34 L35 N187 F218 Y219 D223
Binding residue
(residue number reindexed from 1)		G27 V28 G29 K30 S31 L32 N180 F205 Y206 D210
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=7.82,Kd=15nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0140663 ATP-dependent FeS chaperone activity
Biological Process
GO:0016226 iron-sulfur cluster assembly

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Molecular Function
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Biological Process
External links
PDB RCSB:3vx3, PDBe:3vx3, PDBj:3vx3
PDBsum3vx3
PubMed23399544
UniProtQ5JIH4

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