Structure of PDB 5tem Chain A Binding Site BS02

Receptor Information
>5tem Chain A (length=266) Species: 216895 (Vibrio vulnificus CMCP6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVRIAVAGAAGRMGRNLVKAAHHNPVAKVAAGSERPESSLVGVDLGELCG
EGKFDVVVCDDLAKQIDQFDVIIDFTAPASTLNNLALCQQYGKSIVIGTT
GFTEEQREQIDLVAQQVPVVMAPNYSVGVNLVFKLLEKAAKVMGDYCDIE
IVEAHHRHKVDAPSGTAIGMGEAIAGAMGNKLSDVAVYAREGITGERTKD
EIGFATIRAGDIVGEHTAMFADIGERVEITHKATDRMTFANGAVKAAVWL
HEKPAGFYTMTDVLGL
Ligand information
Ligand IDPDC
InChIInChI=1S/C7H5NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
InChIKeyWJJMNDUMQPNECX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)c1nc(C(=O)O)ccc1
CACTVS 3.341OC(=O)c1cccc(n1)C(O)=O
OpenEye OEToolkits 1.5.0c1cc(nc(c1)C(=O)O)C(=O)O
FormulaC7 H5 N O4
NamePYRIDINE-2,6-DICARBOXYLIC ACID;
DIPICOLINIC ACID
ChEMBLCHEMBL284104
DrugBankDB04267
ZINCZINC000000105246
PDB chain5tem Chain A Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5tem Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T100 P123 H156 K159 S164 G165 T166
Binding residue
(residue number reindexed from 1)		T100 P123 H156 K159 S164 G165 T166
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H155 K159
Catalytic site (residue number reindexed from 1) H155 K159
Enzyme Commision number 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.
Gene Ontology
Molecular Function
GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
GO:0016491 oxidoreductase activity
GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
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:5tem, PDBe:5tem, PDBj:5tem
PDBsum5tem
PubMed32980502
UniProtQ8DEM0|DAPB_VIBVU 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)

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