Structure of PDB 5ok4 Chain A Binding Site BS03

Receptor Information
>5ok4 Chain A (length=344) Species: 79929 (Methanothermobacter marburgensis str. Marburg) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLAILGAGCYRTHAASGITNFSRACEVAEMVGKPEIAMTHSTITMGAEL
KELAGVDEVVVADPVFDNQFTVIDDFAYEDVIEAHKEDPEKIMPQIREKV
NEVAKELPKPPEGAIHFTHPEDLGFEITTDDREAVADADFIMTWFPKGDM
QPDIINKFIDDIKPGAIVTHACTIPTTKFYKIFEQKHGDLVTKPETLNVT
SYHPGAVPEMKGQVYIAEGYASEDAIETLFELGQKARGNAYRLPAELLGP
VCDMCSALTAITYAGILSYRDSVTQVLGAPASFAQMMAKESLEQITALME
KVGIDKMEENLDPGALLGTADSMNFGASAEILPTVFEILEKRKK
Ligand information
Ligand IDFEG
InChIInChI=1S/C19H23N6O11P/c1-6-8(3-10(26)27)22-16(30)7(2)14(6)36-37(32,33)34-4-9-12(28)13(29)18(35-9)25-5-21-11-15(25)23-19(20)24-17(11)31/h5,9,12-13,18,28-29H,3-4H2,1-2H3,(H,22,30)(H,26,27)(H,32,33)(H3,20,23,24,31)/t9-,12-,13-,18-/m1/s1
InChIKeyGTHOTKPHMGEHFD-ACDAHVMNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(nc(c(c1O[P@@](=O)(O)OCC2[C@H]([C@H](C(O2)n3cnc4c3N=C(NC4=O)N)O)O)C)O)CC(=O)O
ACDLabs 10.04O=C(O)Cc4nc(O)c(c(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)c4C)C
CACTVS 3.341Cc1c(O)nc(CC(O)=O)c(C)c1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N
CACTVS 3.341Cc1c(O)nc(CC(O)=O)c(C)c1O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N
OpenEye OEToolkits 1.5.0Cc1c(nc(c(c1OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)C)O)CC(=O)O
FormulaC19 H23 N6 O11 P
Name5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine
ChEMBL
DrugBank
ZINCZINC000058650286
PDB chain5ok4 Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ok4 Dioxygen Sensitivity of [Fe]-Hydrogenase in the Presence of Reducing Substrates.
Resolution1.29 Å
Binding residue
(original residue number in PDB)		L6 G9 H14 A62 D63 P64 P110 P111 D131 W144 F145 I154 A171 C172 H203
Binding residue
(residue number reindexed from 1)		L6 G9 H14 A62 D63 P64 P110 P111 D131 W144 F145 I154 A171 C172 H203
Annotation score1
Enzymatic activity
Enzyme Commision number 1.12.98.2: 5,10-methenyltetrahydromethanopterin hydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0047068 N5,N10-methenyltetrahydromethanopterin hydrogenase activity
Biological Process
GO:0006730 one-carbon metabolic process
GO:0015948 methanogenesis
GO:0019386 methanogenesis, from carbon dioxide

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Molecular Function
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Biological Process
External links
PDB RCSB:5ok4, PDBe:5ok4, PDBj:5ok4
PDBsum5ok4
PubMed29462510
UniProtP32440|HMD_METTM 5,10-methenyltetrahydromethanopterin hydrogenase (Gene Name=hmd)

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