Structure of PDB 2dgk Chain A Binding Site BS01

Receptor Information
>2dgk Chain A (length=438) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDL
SINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSE
ACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELR
EIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALD
KFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFG
LAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQY
YEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAV
CFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRG
FEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain2dgk Chain A Residue 1500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2dgk Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G125 S126 S127 Q163 T212 D243 A245 S273 H275 K276 H465
Binding residue
(residue number reindexed from 1)		G97 S98 S99 Q135 T184 D215 A217 S245 H247 K248 H437
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.15: glutamate decarboxylase.
Gene Ontology
Molecular Function
GO:0004351 glutamate decarboxylase activity
GO:0005515 protein binding
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006536 glutamate metabolic process
GO:0006538 glutamate catabolic process
GO:0019752 carboxylic acid metabolic process
GO:0051454 intracellular pH elevation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2dgk, PDBe:2dgk, PDBj:2dgk
PDBsum2dgk
PubMed16675957
UniProtP69910|DCEB_ECOLI Glutamate decarboxylase beta (Gene Name=gadB)

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