SMTL ID : 5uej.1

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.71, D.104, E.139, E.167 Ligands: ZN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.71, A:D.104, A:E.167, A:E.167, H2O.14 ZN.2: 4 residues within 4Å: Chain A: D.104, E.139, H.353 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.104, A:E.139, A:E.139, A:H.353, H2O.14 ZN.5: 4 residues within 4Å: Chain B: D.104, E.139, H.353 Ligands: ZN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.104, B:E.139, B:E.139, B:H.353, H2O.35 ZN.6: 5 residues within 4Å: Chain B: H.71, D.104, E.139, E.167 Ligands: ZN.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.71, B:D.104, B:E.167, B:E.167, H2O.35 ZN.7: 1 residues within 4Å: Chain B: H.123 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.123, H2O.36, H2O.39

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

SO4.3: 7 residues within 4Å: Chain A: R.182, T.326, G.327, G.328, N.349, I.352 Chain B: Y.201 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.328, A:N.349, B:Y.201 Water bridges: A:R.182, A:R.182, A:T.326, A:T.329, A:N.349, B:Y.201 Salt bridges: A:K.179, A:R.182 SO4.4: 3 residues within 4Å: Chain A: S.185, R.262, S.294 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.185, A:S.294, A:S.294 Water bridges: A:S.187, A:N.260, A:R.262, A:R.262, B:T.248, B:T.248 Salt bridges: A:R.262 SO4.8: 3 residues within 4Å: Chain B: S.185, R.262, S.294 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.185, B:S.185, B:S.294 Water bridges: B:S.187, B:N.260, B:R.262, B:R.262, B:R.262, A:N.249 Salt bridges: B:R.262 SO4.9: 5 residues within 4Å: Chain A: Y.201 Chain B: K.179, R.182, G.327, G.328 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.328, A:Y.201 Water bridges: B:P.168, B:P.168, B:K.179, B:R.182, B:R.182, B:N.349, A:Y.201 Salt bridges: B:K.179, B:R.182 SO4.10: 2 residues within 4Å: Chain B: A.311, R.377 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., 1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58. To Be Published

Release Date

2017-02-01

Peptides

Succinyl-diaminopimelate desuccinylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinyl-diaminopimelate desuccinylase

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