Structure of PDB 1ko0 Chain A Binding Site BS03

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 IDDLY
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1
InChIKeyKDXKERNSBIXSRK-RXMQYKEDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCC[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCCN
CACTVS 3.341NCCCC[CH](N)C(O)=O
OpenEye OEToolkits 1.5.0C(CCN)CC(C(=O)O)N
OpenEye OEToolkits 1.5.0C(CCN)C[C@H](C(=O)O)N
FormulaC6 H14 N2 O2
NameD-LYSINE
ChEMBLCHEMBL319497
DrugBankDB03252
ZINCZINC000001532731
PDB chain1ko0 Chain A Residue 542 [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)		K54 T157 H191 Y311 Y378
Binding residue
(residue number reindexed from 1)		K53 T156 H190 Y310 Y377
Annotation score5
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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