SMTL ID : 4op4.1 (1 other biounit)

Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: D.257, Q.260, K.261, N.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.257, A:K.261, A:N.264 EDO.8: 5 residues within 4Å: Chain A: D.160, M.161, T.190, E.192, Q.229 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.160, A:D.160, A:T.190, A:E.192, A:Q.229 Water bridges: A:T.190 EDO.11: 8 residues within 4Å: Chain A: H.70, D.103, E.137, E.138, E.166, H.241 Ligands: ZN.2, ZN.3 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.103, E.138, H.241 Ligands: ZN.3, EDO.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.103, A:E.138, A:E.138, A:H.241 ZN.3: 7 residues within 4Å: Chain A: H.70, D.103, E.137, E.138, E.166 Ligands: ZN.2, EDO.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.70, A:D.103, A:E.166, A:E.166

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.147, E.150, T.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.147, A:R.147 GOL.9: 5 residues within 4Å: Chain A: A.38, L.39, G.40, R.58, I.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.58 Water bridges: A:I.119

4 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.5: 5 residues within 4Å: Chain A: L.79, W.82, H.83, T.84, P.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.79 BU1.6: 10 residues within 4Å: Chain A: V.149, L.152, M.153, E.157, L.158, I.159, I.223, M.226, G.227, A.228 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.149, A:M.226 Hydrogen bonds: A:E.157, A:I.159 Water bridges: A:I.159, A:R.182 BU1.7: 7 residues within 4Å: Chain A: K.178, T.214, G.215, G.216, G.220, R.221, V.230 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.178 Hydrogen bonds: A:G.216 Water bridges: A:T.217, A:E.232 BU1.10: 2 residues within 4Å: Chain A: D.93, G.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., The Dimerization Domain in DapE Enzymes Is required for Catalysis. Plos One (2014)

Release Date

2014-04-23

Peptides

Succinyl-diaminopimelate desuccinylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Succinyl-diaminopimelate desuccinylase

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