SMTL ID : 2gke.1

Crystal structure of diaminopimelate epimerase in complex with an irreversible inhibitor LL-AziDAP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x ZDP: (2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID(Covalent)

ZDP.1: 16 residues within 4Å: Chain A: N.11, F.13, Q.44, N.64, V.70, Q.72, C.73, G.74, N.75, N.157, N.190, E.208, R.209, C.217, G.218, S.219 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.13, A:Q.44, A:V.70 Hydrogen bonds: A:N.11, A:N.11, A:Q.44, A:N.64, A:N.64, A:G.74, A:N.75, A:N.157, A:N.190, A:E.208, A:G.218, A:S.219, A:S.219 Salt bridges: A:R.209

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: E.124, N.133, K.134, F.135 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.124, A:N.133, A:F.135

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: Y.139, I.140, R.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.140 Water bridges: A:N.133 Salt bridges: A:R.184 ACY.4: 1 residues within 4Å: Chain A: H.256 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.256 ACY.5: 3 residues within 4Å: Chain A: G.255, H.256, P.257 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pillai, B. et al., Structural insights into stereochemical inversion by diaminopimelate epimerase: An antibacterial drug target. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-05-16

Peptides

Diaminopimelate epimerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Diaminopimelate epimerase

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