SMTL ID : 3o3p.1

Crystal structure of R. xylanophilus MpgS in complex with GDP-Mannose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: R.325, S.353, E.373, L.374 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: R.325, R.329, R.332 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: Q.351, D.354 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.351, A:D.354, H2O.2, H2O.2, H2O.4, H2O.4 MG.4: 3 residues within 4Å: Chain A: D.189, N.308 Ligands: GDD.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.189

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

GDD.5: 23 residues within 4Å: Chain A: P.101, S.102, R.103, V.105, V.132, D.133, A.134, E.154, G.166, K.167, A.170, D.187, A.188, D.189, L.259, A.260, G.261, Y.279, E.282, N.308, Q.311, M.319 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.102, A:R.103, A:R.103, A:V.132, A:D.187, A:A.188, A:D.189, A:G.261, A:Y.279, A:N.308 Water bridges: A:G.166, A:G.166, A:K.167, A:K.167 Salt bridges: A:E.154

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

GDP.6: 16 residues within 4Å: Chain B: P.101, S.102, R.103, V.105, V.132, D.133, A.134, E.154, G.166, K.167, A.170, D.187, A.188, D.189, Y.279, Q.311 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:S.102, B:R.103, B:V.132, B:A.188, B:D.189, B:D.189, B:Y.279 Water bridges: B:E.154, B:G.166, B:K.167 Salt bridges: B:E.154, B:K.167, B:K.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Empadinhas, N. et al., Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity. Mol.Microbiol. (2011)

Release Date

2010-11-03

Peptides

Mannosyl-3-phosphoglycerate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mannosyl-3-phosphoglycerate synthase

Related Entries With Identical Sequence