Structure of PDB 8q5x Chain B Binding Site BS02

Receptor Information
>8q5x Chain B (length=280) Species: 267377 (Methanococcus maripaludis S2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRKIAIYGKGGIGKSTTTQNTVAAMAHFHDKKVFIHGCDPKADSTRLILH
GKQQVTMMDTLREKGEDECTPDKVIEVGFGGVKCVESGGPEPGVGCAGRG
VITAITLMEQHGVYEDDLDFVFFDVLGDVVCGGFAMPVRDGKADEIYVVA
SGEMMALYAANNICKGMVKYAEQSGVRLGGIICNSRNVDGELDLLQEFCD
KIGTQLIHFVPRDNIVQKAEFQKKAVVDYDDTCNQALEYKELARKIIENE
NLVIPTPMTMDELEELTSKYGFLDGRAIEG
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 chain8q5x Chain B Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8q5x Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G12 I13 G14 K15 S16 T17 N185 D214 V217 Q218 E221
Binding residue
(residue number reindexed from 1)		G11 I12 G13 K14 S15 T16 N184 D213 V216 Q217 E220
Annotation score5
Enzymatic activity
Enzyme Commision number 1.18.6.1: nitrogenase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016163 nitrogenase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009399 nitrogen fixation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8q5x, PDBe:8q5x, PDBj:8q5x
PDBsum8q5x
PubMed38696373
UniProtP0CW57|NIFH_METMP Nitrogenase iron protein (Gene Name=nifH)

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