SMTL ID : 3o61.1 (1 other biounit)

Structure of the E100A E.coli GDP-mannose hydrolase (yffh) in complex with GDP-mannose and Mg++

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x GDD: GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE(Non-covalent)

GDD.1: 22 residues within 4Å: Chain A: Y.17, F.18, R.44, G.47, A.48, Q.65, R.67, A.85, G.86, L.87, E.104, E.127, I.129, E.151, K.176 Chain B: K.38, R.39, E.40, S.121, P.122, G.123 Ligands: MG.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.44, A:R.44, A:A.48, A:A.48, A:Q.65, A:G.86, A:L.87, A:E.127, B:E.40, B:S.121 Salt bridges: A:R.67, A:R.67, A:K.176 pi-Stacking: A:Y.17 pi-Cation interactions: A:Y.17, B:R.39, B:R.39 Water bridges: B:R.39 GDD.4: 22 residues within 4Å: Chain A: K.38, R.39, E.40, S.121, P.122, G.123 Chain B: Y.17, F.18, R.44, N.46, G.47, A.48, R.67, A.85, G.86, L.87, E.104, E.127, I.129, E.151, K.176 Ligands: MG.5 18 PLIP interactions: 7 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.39, A:E.40, A:S.121, B:R.44, B:A.48, B:A.48, B:L.87 Water bridges: A:R.39, A:G.123, B:Q.65, B:Q.65, B:A.85 pi-Cation interactions: A:R.39, A:R.39, B:Y.17 Salt bridges: B:R.67, B:R.67 pi-Stacking: B:Y.17

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.65, A.85, E.104 Ligands: GDD.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.85, A:E.104, A:E.104, H2O.1 MG.5: 3 residues within 4Å: Chain B: A.85, E.104 Ligands: GDD.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:A.85, B:E.104, H2O.2, H2O.3

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: T.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boto, A.N. et al., Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals a new motif for mannose recognition. Proteins (2011)

Release Date

2011-05-11

Peptides

GDP-mannose pyrophosphatase nudK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-mannose pyrophosphatase nudK

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