Structure of PDB 8q5w Chain D Binding Site BS02

Receptor Information
>8q5w Chain D (length=277) Species: 573063 (Methanocaldococcus infernus ME) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEIAPNAKKVAIYGKGGIGKSTTTQNTAAALAYYYKLKGMIHGCDPKADS
TRMILHGKPQETVMDVLREEGEEGVTLEKVRKVGFCGIYCVESGGPEPGV
GCAGRGVITAVNLMKELGGYPDDLDFLFFDVLGDVVCGGFAMPLRDGLAK
EIYIVSSGEMMALYAANNIAKGILKYAEQSGVRLGGIICNSRNVDGEREL
MEEFCDKLGTKLIHFIPRDNIVQKAEFNKMTVVEFAPDHPQALEYKKLGK
KIMDNDELVIPTPLSMDELEKLVEKYG
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 chain8q5w Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8q5w Structural comparison of (hyper-)thermophilic nitrogenase reductases from three marine Methanococcales.
Resolution2.49 Å
Binding residue
(original residue number in PDB)		G20 G22 K23 S24 T25 N193 R221 D222 V225
Binding residue
(residue number reindexed from 1)		G17 G19 K20 S21 T22 N190 R218 D219 V222
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:8q5w, PDBe:8q5w, PDBj:8q5w
PDBsum8q5w
PubMed38696373
UniProtD5VUA1

[Back to BioLiP]