Structure of PDB 1zc9 Chain A Binding Site BS01

Receptor Information
>1zc9 Chain A (length=431) Species: 292 (Burkholderia cepacia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQ
MSAVLGHCHPEIVSVIGEYAGKLDHLFSEMLSRPVVDLATRLANITPPGL
DRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSA
GRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSG
NLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRT
GTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYT
THVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIG
DVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMG
GVFRIAPPLTVSEDEIDLGLSLLGQAIERAL
Ligand information
Ligand IDPMP
InChIInChI=1S/C8H13N2O5P/c1-5-8(11)7(2-9)6(3-10-5)4-15-16(12,13)14/h3,11H,2,4,9H2,1H3,(H2,12,13,14)
InChIKeyZMJGSOSNSPKHNH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1CN)C
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN)c1O
FormulaC8 H13 N2 O5 P
Name4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE;
PYRIDOXAMINE-5'-PHOSPHATE
ChEMBLCHEMBL1235353
DrugBankDB02142
ZINCZINC000001532708
PDB chain1zc9 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1zc9 Role of q52 in catalysis of decarboxylation and transamination in dialkylglycine decarboxylase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G111 A112 W138 H139 E210 D243 A245 Q246 K272
Binding residue
(residue number reindexed from 1)		G109 A110 W136 H137 E208 D241 A243 Q244 K270
Annotation score1
Binding affinityMOAD: Kd=0.6mM
PDBbind-CN: -logKd/Ki=3.22,Kd=0.6mM
Enzymatic activity
Catalytic site (original residue number in PDB) G21 W138 E210 D243 Q246 K272 T303 R406
Catalytic site (residue number reindexed from 1) G19 W136 E208 D241 Q244 K270 T301 R404
Enzyme Commision number 4.1.1.64: 2,2-dialkylglycine decarboxylase (pyruvate).
Gene Ontology
Molecular Function
GO:0008453 alanine-glyoxylate transaminase activity
GO:0008483 transaminase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0047432 2,2-dialkylglycine decarboxylase (pyruvate) activity
Biological Process
GO:0009436 glyoxylate catabolic process
GO:0019481 L-alanine catabolic process, by transamination

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1zc9, PDBe:1zc9, PDBj:1zc9
PDBsum1zc9
PubMed16342932
UniProtP16932|DGDA_BURCE 2,2-dialkylglycine decarboxylase (Gene Name=dgdA)

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