SMTL ID : 3ic1.1

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.67, D.100, E.134, E.135, E.163 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.67, A:D.100, A:E.163, A:E.163, H2O.4 ZN.2: 4 residues within 4Å: Chain A: D.100, E.135, H.349 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.100, A:E.135, A:E.135, A:H.349, H2O.4 ZN.10: 4 residues within 4Å: Chain B: D.100, E.135, H.349 Ligands: ZN.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.100, B:E.135, B:E.135, B:H.349, H2O.8 ZN.11: 6 residues within 4Å: Chain B: H.67, D.100, E.134, E.135, E.163 Ligands: ZN.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.67, B:D.100, B:E.163, B:E.163, H2O.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: K.269, E.286, W.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.269, A:W.287 GOL.6: 3 residues within 4Å: Chain B: L.344, S.356, D.359 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.356, B:S.356, B:D.359 Water bridges: B:S.356

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain A: R.178, R.179, R.258, G.322, G.323, G.324 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.322, A:G.324 Water bridges: A:R.179, A:R.179 Salt bridges: A:R.178, A:R.179, A:R.258 SO4.5: 2 residues within 4Å: Chain A: G.299, K.300 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.300, A:E.337 Salt bridges: A:K.300 SO4.7: 3 residues within 4Å: Chain B: R.258, T.325, R.329 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.329, B:R.329 Salt bridges: B:R.258, B:R.329 SO4.8: 2 residues within 4Å: Chain B: G.323, G.324 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.324 SO4.9: 4 residues within 4Å: Chain B: R.178, R.179, R.258, G.322 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.179 Water bridges: B:R.179, B:R.179 Salt bridges: B:R.178, B:R.179, B:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B.P. et al., Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase. J.Mol.Biol. (2010)

Release Date

2009-09-22

Peptides

Succinyl-diaminopimelate desuccinylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinyl-diaminopimelate desuccinylase

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