Structure of PDB 8q5x Chain D Binding Site BS01

Receptor Information
>8q5x Chain D (length=278) 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
NLVIPTPMTMDELEELTSKYGFLDGRAI
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)		D275 G276 R277
Binding residue
(residue number reindexed from 1)		D274 G275 R276
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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