SMTL ID : 4k2s.2 (3 other biounits)

Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GCO: D-gluconic acid(Non-covalent)

GCO.1: 18 residues within 4Å: Chain A: N.39, H.124, R.149, Y.161, D.213, H.215, E.239, E.265, R.286, H.315, A.317, D.319, E.342, L.392, W.405 Chain B: Y.77, W.78 Ligands: MG.2 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.39, A:Y.161, A:Y.161, A:H.215, A:E.265, B:Y.77 Water bridges: A:R.149, A:R.149, A:Y.161, A:T.318 Salt bridges: A:H.124, A:R.149, A:R.286, A:H.315 GCO.5: 18 residues within 4Å: Chain A: Y.77, W.78 Chain B: N.39, H.124, R.149, Y.161, D.213, H.215, E.239, E.265, R.286, H.315, A.317, D.319, E.342, L.392, W.405 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.39, B:Y.161, B:Y.161, B:H.215, B:E.265 Water bridges: B:Y.122, B:Y.122, B:H.124, B:Y.161, B:T.318, A:Y.77 Salt bridges: B:H.124, B:R.149, B:R.286, B:H.315

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 5 residues within 4Å: Chain A: D.213, E.239, E.265, R.286 Ligands: GCO.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:E.239, A:E.265, H2O.14 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain B: D.213, E.239, E.265, R.286 Ligands: GCO.5 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.213, B:E.239, B:E.265, H2O.30 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.104, M.105, P.106, Q.109, E.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.104, A:Q.109, A:E.369

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 8 residues within 4Å: Chain A: G.81, P.82, V.83, T.84 Chain B: G.81, P.82, V.83, T.84 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: W.184, L.397, E.398 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fedorov, A.A. et al., Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate. To be Published

Release Date

2014-04-09

Peptides

D-mannonate dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

D-mannonate dehydratase

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