SMTL ID : 2gt4.2 (1 other biounit)

Crystal Structure of the Y103F mutant of the GDP-mannose mannosyl hydrolase in complex with GDP-mannose and MG+2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BMA: beta-D-mannopyranose(Post Translational Modification)

BMA.1: 7 residues within 4Å: Chain A: K.36, R.37, T.38, N.39, R.40 Ligands: MG.2, GDD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.37, A:T.38, A:T.38, A:N.39 Water bridges: A:K.36, A:E.70, A:E.70, A:Y.127 BMA.4: 7 residues within 4Å: Chain B: K.36, R.37, T.38, N.39, R.40 Ligands: MG.5, GDD.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.37, B:T.38, B:T.38, B:N.39 Water bridges: B:K.36, B:E.70, B:E.70, B:Y.127

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: G.50, G.51, E.70 Ligands: BMA.1, GDD.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.50, A:E.70, H2O.1, H2O.1 MG.5: 5 residues within 4Å: Chain B: G.50, G.51, E.70 Ligands: BMA.4, GDD.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:G.50, B:E.70, H2O.6, H2O.6

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

GDD.3: 20 residues within 4Å: Chain A: F.3, L.4, Q.6, F.9, S.20, D.22, R.37, N.39, F.47, G.50, G.51, R.52, E.70, H.88, Y.90, F.94, F.103, V.105 Ligands: BMA.1, MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.4, A:L.4, A:L.4, A:S.20, A:S.20, A:N.39, A:G.50, A:R.52, A:R.52, A:Y.90, A:Y.90 Water bridges: A:G.50, A:G.50, A:E.70 pi-Stacking: A:F.3, A:F.9, A:F.9 GDD.6: 20 residues within 4Å: Chain B: F.3, L.4, Q.6, F.9, S.20, D.22, R.37, N.39, F.47, G.50, G.51, R.52, E.70, H.88, Y.90, F.94, F.103, V.105 Ligands: BMA.4, MG.5 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:L.4, B:L.4, B:L.4, B:S.20, B:S.20, B:N.39, B:G.50, B:R.52, B:R.52, B:H.88, B:Y.90 Water bridges: B:G.50, B:G.50, B:E.70, B:E.70 pi-Stacking: B:F.3, B:F.9, B:F.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabelli, S.B. et al., X-ray, NMR, and mutational studies of the catalytic cycle of the GDP-mannose mannosyl hydrolase reaction. Biochemistry (2006)

Release Date

2006-12-12

Peptides

GDP-mannose mannosyl hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

GDP-mannose mannosyl hydrolase

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