Structure of PDB 5gmd Chain A Binding Site BS01

Receptor Information
>5gmd Chain A (length=325) Species: 273057 (Saccharolobus solfataricus P2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKSVTVSAPSNIAVVKYWGKRGDERLNLPLNNSLSITLDDQLSVITKVT
LNDKNIVIVNDRILSEDEMKEYAGRVLDTFKKIVGKEFHVKVESKSKFPI
NAGLASSAAGIAALAFSLNELLELNLKSEELSKIARLGSGSACRSMFGGF
VVWNKGEREDGEDSYCYQIFRHDYWSELVDIIPILSEKEKKISSRKGMIR
SAETSELMECRLKYIEKTFNEVIEAIRNRDEKKFYYLMMRHSNSMHAVIL
DSWPSFFYLNDTSIRIMEWIHDYGKAGYTFDAGPNPHIFTTERNIGDILE
FLKSLEIKRIIVSKVGDGPKVLSRE
Ligand information
Ligand IDDP6
InChIInChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1
InChIKeySIGQQUBJQXSAMW-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@](CCO[P@@](=O)(O)OP(=O)(O)O)(CC(=O)O)O
ACDLabs 10.04O=P(OP(=O)(OCCC(O)(C)CC(=O)O)O)(O)O
OpenEye OEToolkits 1.5.0CC(CCOP(=O)(O)OP(=O)(O)O)(CC(=O)O)O
CACTVS 3.341C[C@@](O)(CCO[P@](O)(=O)O[P](O)(O)=O)CC(O)=O
CACTVS 3.341C[C](O)(CCO[P](O)(=O)O[P](O)(O)=O)CC(O)=O
FormulaC6 H14 O10 P2
Name(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID
ChEMBLCHEMBL235881
DrugBank
ZINCZINC000008216889
PDB chain5gmd Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5gmd A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase
Resolution1.5 Å
Binding residue
(original residue number in PDB)		A14 Y18 W19 K21 N28 S139 G140 S141 R144 R195 M198 D281
Binding residue
(residue number reindexed from 1)		A14 Y18 W19 K21 N28 S139 G140 S141 R144 R195 M198 D281
Annotation score5
Enzymatic activity
Enzyme Commision number 4.1.1.33: diphosphomevalonate decarboxylase.
Gene Ontology
Molecular Function
GO:0004163 diphosphomevalonate decarboxylase activity
GO:0005524 ATP binding
GO:0016829 lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5gmd, PDBe:5gmd, PDBj:5gmd
PDBsum5gmd
PubMed28003359
UniProtQ97UL5|DMD_SACS2 Diphosphomevalonate decarboxylase (Gene Name=SSO2989)

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