SMTL ID : 3o52.3 (2 other biounits)

Structure of the E.coli GDP-mannose hydrolase (yffh) in complex with tartrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.1: 10 residues within 4Å: Chain A: R.44, R.67, L.87, E.127, I.129, K.176 Chain B: S.121, P.122, G.123 Ligands: NA.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.127, B:G.123 Water bridges: A:R.67, A:R.67, A:K.176 Salt bridges: A:R.44, A:R.67, A:K.176 TAR.4: 10 residues within 4Å: Chain A: S.121, P.122, G.123 Chain B: R.44, R.67, L.87, E.127, I.129, K.176 Ligands: NA.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.82, B:E.127, A:G.123 Water bridges: B:R.67, B:R.67, B:K.176 Salt bridges: B:R.44, B:R.67, B:K.176

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

NA.2: 2 residues within 4Å: Chain A: R.67 Ligands: TAR.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.67, A:R.67 NA.5: 2 residues within 4Å: Chain B: R.67 Ligands: TAR.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.67, B:R.67

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

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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
E

B
E

GDP-mannose pyrophosphatase nudK

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