Structure of PDB 3daf Chain A Binding Site BS03

Receptor Information
>3daf Chain A (length=344) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKIAILGAGCYRTHAAAGITNFMRACEVAKEVGKPEIALTHSSITYGAEL
LHLVPDVKEVIVSDPCFAEEPGLVVIDEFDPKEVMEAHLSGNPESIMPKI
REVVKAKAKELPKPPKACIHLVHPEDVGLKVTSDDREAVEGADIVITWLP
KGNKQPDIIKKFADAIPEGAIVTHACTIPTTKFAKIFKDLGREDLNITSY
HPGCVPEMKGQVYIAEGYASEEAVNKLYEIGKIARGKAFKMPANLIGPVC
DMCSAVTATVYAGLLAYRDAVTKILGAPADFAQMMADEALTQIHNLMKEK
GIANMEEALDPAALLGTADSMCFGPLAEILPTALKVLEVHKVVE
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 chain3daf Chain A Residue 501 [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]
PDB3daf The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G7 G9 T13 H14 S63 D64 P65 P114 P115 C118 D135 W148 L149 P150 I158 C176 T177
Binding residue
(residue number reindexed from 1)		G7 G9 T13 H14 S63 D64 P65 P114 P115 C118 D135 W148 L149 P150 I158 C176 T177
Annotation score1
Enzymatic activity
Enzyme Commision number 1.12.98.2: 5,10-methenyltetrahydromethanopterin hydrogenase.
Gene Ontology
Molecular Function
GO:0004735 pyrroline-5-carboxylate reductase activity
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
GO:0055129 L-proline biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3daf, PDBe:3daf, PDBj:3daf
PDBsum3daf
PubMed18653896
UniProtQ58194|HMD_METJA 5,10-methenyltetrahydromethanopterin hydrogenase (Gene Name=hmd)

[Back to BioLiP]