SMTL ID : 3o6z.1

Structure of the D152A E.coli GDP-mannose hydrolase (yffh) in complex with Mg++

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: A.85, E.104 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.85, A:E.104, H2O.5, H2O.5, H2O.6 MG.2: 5 residues within 4Å: Chain B: A.85, E.100, E.104, E.151 Ligands: MG.3 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.100, B:E.104, B:E.151, H2O.7, H2O.13, H2O.13 MG.3: 4 residues within 4Å: Chain B: A.85, E.104, E.151 Ligands: MG.2 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:A.85, B:E.104, H2O.7, H2O.8, H2O.12, H2O.13

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

CL.4: 2 residues within 4Å: Chain B: R.113, L.189 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: Q.3, Q.4, T.28 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain B: E.94, V.95, R.98, K.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.99 PEG.8: 4 residues within 4Å: Chain B: D.15, T.19, H.21, D.43 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.43

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 6 residues within 4Å: Chain B: R.64, I.81, L.156, Q.162, M.166, E.171 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.162, B:E.171, B:E.171 Water bridges: B:R.64

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