Structure of PDB 1ko0 Chain A Binding Site BS01

Receptor Information
>1ko0 Chain A (length=419) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRF
AQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTA
DVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPGFGHGH
SQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHL
EQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAA
REQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAG
FNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQ
EGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQ
ARLIRRRQTIEELLALELL
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 chain1ko0 Chain A Residue 540 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ko0 Diaminopimelate Decarboxylase uses a Versatile Active Site for Stereospecific Decarboxylation
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A52 K54 H191 G227 E268 P269 G270 R271 Y378
Binding residue
(residue number reindexed from 1)		A51 K53 H190 G226 E267 P268 G269 R270 Y377
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.20: diaminopimelate decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005515 protein binding
GO:0008836 diaminopimelate decarboxylase activity
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1ko0, PDBe:1ko0, PDBj:1ko0
PDBsum1ko0
PubMed
UniProtP00861|DCDA_ECOLI Diaminopimelate decarboxylase (Gene Name=lysA)

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