SMTL ID : 5e3r.1

Crystal structure of DapD in complex with 2-aminopimelate from Corynebacterium glutamicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x NPI: (2S)-2-aminoheptanedioic acid(Non-covalent)

NPI.1: 10 residues within 4Å: Chain A: R.142, M.162, M.178, E.180 Chain C: F.89, R.150, F.166, N.168, S.184, A.185 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.89 Hydrogen bonds: C:N.168, C:A.185 Salt bridges: C:R.150, A:R.142 NPI.2: 10 residues within 4Å: Chain A: F.89, R.150, F.166, N.168, S.184, A.185 Chain B: R.142, M.162, M.178, E.180 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.89 Hydrogen bonds: A:N.168, A:A.185 Salt bridges: A:R.150, B:R.142 NPI.3: 10 residues within 4Å: Chain B: F.89, R.150, F.166, N.168, S.184, A.185 Chain C: R.142, M.162, M.178, E.180 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.89 Hydrogen bonds: B:N.168, B:A.185 Salt bridges: B:R.150, C:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sagong, H.Y. et al., Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum. J.Agric.Food Chem. (2015)

Release Date

2015-11-04

Peptides

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

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