SMTL ID : 1rya.1

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: G.50, G.51, E.70, Q.123 Ligands: GDP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.50, A:E.70, H2O.1 MG.4: 5 residues within 4Å: Chain B: G.50, G.51, E.70, Q.123 Ligands: GDP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.50, B:E.70, H2O.15

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 14 residues within 4Å: Chain A: F.3, L.4, F.9, R.37, N.39, G.50, G.51, R.52, E.70, F.94, Y.103, Q.123 Ligands: MG.1, TRS.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.4, A:L.4, A:L.4, A:N.39, A:R.52, A:R.52, A:Q.123 Water bridges: A:R.37, A:R.37, A:R.37, A:N.39, A:Y.103, A:Y.103 Salt bridges: A:R.37 pi-Stacking: A:F.3, A:F.9, A:F.9 GDP.6: 15 residues within 4Å: Chain B: F.3, L.4, Q.6, F.9, R.37, N.39, G.50, G.51, R.52, E.70, F.94, Y.103, Q.123 Ligands: MG.4, TRS.7 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:L.4, B:L.4, B:L.4, B:G.50, B:R.52, B:R.52, B:Y.103, B:Q.123 Water bridges: B:Q.6, B:Q.6, B:Q.6, B:R.37, B:R.37, B:R.37, B:N.39, B:N.39, B:N.39, B:N.39, B:E.70 Salt bridges: B:R.37 pi-Stacking: B:F.3, B:F.9, B:F.9

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

TRS.3: 8 residues within 4Å: Chain A: S.20, D.22, R.37, F.47, H.88, Y.90, Y.103 Ligands: GDP.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.20, A:L.21, A:D.22, A:H.88, A:Y.90 Water bridges: A:R.37, A:P.41 TRS.7: 8 residues within 4Å: Chain B: S.20, D.22, R.37, F.47, H.88, Y.90, Y.103 Ligands: GDP.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.20, B:S.20, B:D.22, B:H.88

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

CL.5: 4 residues within 4Å: Chain B: N.27, S.28, S.113, E.114 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabelli, S.B. et al., Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus. Structure (2004)

Release Date

2004-06-22

Peptides

GDP-mannose mannosyl hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

GDP-mannose mannosyl hydrolase

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