Structure of PDB 5m47 Chain A Binding Site BS01

Receptor Information
>5m47 Chain A (length=280) Species: 196627 (Corynebacterium glutamicum ATCC 13032) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNLTIPFAKGHATENDFIIIPDEDARLDLTPEMVVTLCDRRAGIGADGIL
RVVKAADVEGSTVDPSLWFMDYRNADGSLAEMCGNGVRLFAHWLYSRGLV
DNTSFDIGTRAGVRHVDILQADQHSAQVRVDMGIPDVTGLSTCDINGQVF
AGLGVDMGNPHLACVVPGLSASALADMELRAPTFDQEFFPHGVNVEIVTE
LEDDAVSMRVWERGVGETRSCGTGTVAAACAALADAGLGEGTVKVCVPGG
EVEVQIFDDGSTLTGPSAIIALGEVQIHHH
Ligand information
Ligand IDAPI
InChIInChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
InChIKeyGMKMEZVLHJARHF-SYDPRGILSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH](CCC[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.2C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
OpenEye OEToolkits 1.7.2C(CC(C(=O)O)N)CC(C(=O)O)N
CACTVS 3.370N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCC(C(=O)O)N
FormulaC7 H14 N2 O4
Name2,6-DIAMINOPIMELIC ACID
ChEMBLCHEMBL415306
DrugBank
ZINCZINC000001532722
PDB chain5m47 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5m47 Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		N15 N74 C83 G84 N85 N159 N194 E212 R213 C221 G222 T223
Binding residue
(residue number reindexed from 1)		N15 N74 C83 G84 N85 N159 N194 E212 R213 C221 G222 T223
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) C83 H161 E212 C221 G224
Catalytic site (residue number reindexed from 1) C83 H161 E212 C221 G224
Enzyme Commision number 5.1.1.7: diaminopimelate epimerase.
Gene Ontology
Molecular Function
GO:0008837 diaminopimelate epimerase activity
GO:0016853 isomerase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5m47, PDBe:5m47, PDBj:5m47
PDBsum5m47
PubMed28176858
UniProtQ8NP73|DAPF_CORGL Diaminopimelate epimerase (Gene Name=dapF)

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