Structure of PDB 8dqv Chain D Binding Site BS01

Receptor Information
>8dqv Chain D (length=322) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASVLWFQGGACSGNTMSFLNADEPNVVDLIVDFGLDLLWHPSLGLELGNN
AQKVFWDCAKGERPLDIFVFEGTVIEAPNGTGQMDMFAGRPMKDWVTDLA
GAAQIVVAIGDCACFGGIPAMEPNPSGSTGLQFHKREKGGFLGPDFRSKM
GLPVINVPGCPAHPDWITQILVALATGRAGDITLDDLHRPETFFKTFTQT
GCTRVQFFEYKQSTLSFGEGTRTGCLFYEFGCRGPMTHSPCNRILWNRQS
SKTRAGMPCLGCTEPEFPHFDLAPGTVFKTQKVSGMIPKEVPEGTDHLTY
MGLAAAARIAAPQWSKEDMFVV
Ligand information
Ligand IDVK3
InChIInChI=1S/C11H8O2/c1-7-6-10(12)8-4-2-3-5-9(8)11(7)13/h2-6H,1H3
InChIKeyMJVAVZPDRWSRRC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341
OpenEye OEToolkits 1.5.0		CC1=CC(=O)c2ccccc2C1=O
ACDLabs 10.04O=C2c1c(cccc1)C(=O)C(=C2)C
FormulaC11 H8 O2
NameMENADIONE;
VITAMIN K3;
2-METHYL-1,4-NAPHTHALENEDIONE
ChEMBLCHEMBL590
DrugBankDB00170
ZINCZINC000000001677
PDB chain8dqv Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8dqv Structural basis for bacterial energy extraction from atmospheric hydrogen.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		K212 Q213 S214 F228 Y229 Y301 M302
Binding residue
(residue number reindexed from 1)		K211 Q212 S213 F227 Y228 Y300 M301
Annotation score1
Enzymatic activity
Enzyme Commision number 1.12.99.6: hydrogenase (acceptor).
Gene Ontology
Molecular Function
GO:0008901 ferredoxin hydrogenase activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0033748 hydrogenase (acceptor) activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051538 3 iron, 4 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic respiration
Cellular Component
GO:0009375 ferredoxin hydrogenase complex
GO:0016020 membrane
GO:0044569 [Ni-Fe] hydrogenase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8dqv, PDBe:8dqv, PDBj:8dqv
PDBsum8dqv
PubMed36890228
UniProtA0QUM6

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