Structure of PDB 1kgt Chain A Binding Site BS01

Receptor Information
>1kgt Chain A (length=274) Species: 1765 (Mycobacterium tuberculosis variant bovis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID
GQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQK
EGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCA
QIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGS
VISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCA
VIVKKVDAKTRGKVGINELLRTID
Ligand information
Ligand IDPML
InChIInChI=1S/C7H12O4/c8-6(9)4-2-1-3-5-7(10)11/h1-5H2,(H,8,9)(H,10,11)
InChIKeyWLJVNTCWHIRURA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CCCCCC(O)=O
ACDLabs 10.04O=C(O)CCCCCC(=O)O
OpenEye OEToolkits 1.5.0C(CCC(=O)O)CCC(=O)O
FormulaC7 H12 O4
NamePIMELIC ACID
ChEMBLCHEMBL1235351
DrugBankDB01856
ZINCZINC000001529489
PDB chain1kgt Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1kgt Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R104 M124 M139
Binding residue
(residue number reindexed from 1)		R104 M124 M139
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D141 G166 E189
Catalytic site (residue number reindexed from 1) D141 G166 E189
Enzyme Commision number 2.3.1.117: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase.
Gene Ontology
Molecular Function
GO:0008666 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1kgt, PDBe:1kgt, PDBj:1kgt
PDBsum1kgt
PubMed11910040
UniProtP56220|DAPD_UNKP 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (Gene Name=dapD)

[Back to BioLiP]