SMTL ID : 4y7g.1

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and glycerol 3-phosphate (G3P) - GpgS Mn2+ UDP-Glc G3P

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 3 residues within 4Å: Chain A: D.140, H.262 Ligands: UPG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:H.262, H2O.1, H2O.1 MN.4: 3 residues within 4Å: Chain B: D.140, H.262 Ligands: UPG.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.140, B:H.262, H2O.4, H2O.4

2 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.2: 6 residues within 4Å: Chain A: G.188, R.189, T.191, R.260, H.262, N.264 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.189, A:T.191, A:T.191, A:R.260, A:N.264 Water bridges: A:T.191, A:R.265 Salt bridges: A:R.189, A:H.262 G3P.5: 6 residues within 4Å: Chain B: G.188, R.189, T.191, R.260, H.262, N.264 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.189, B:T.191, B:T.191, B:R.260, B:N.264 Water bridges: B:T.191, B:R.265 Salt bridges: B:R.189, B:H.262

2 x UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.3: 20 residues within 4Å: Chain A: P.54, A.55, L.56, E.58, S.85, G.117, K.118, D.138, S.139, D.140, L.213, G.215, Y.233, E.236, R.260, H.262, R.263, R.265, M.273 Ligands: MN.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.56 Hydrogen bonds: A:L.56, A:L.56, A:E.58, A:S.85, A:S.85, A:G.117, A:K.118, A:K.118, A:D.138, A:S.139, A:D.140, A:Y.233, A:R.260, A:R.260 Water bridges: A:K.118, A:D.138, A:E.236 Salt bridges: A:H.262, A:R.263, A:R.265, A:R.265 UPG.6: 20 residues within 4Å: Chain B: P.54, A.55, L.56, E.58, S.85, G.117, K.118, D.138, S.139, D.140, L.213, G.215, Y.233, E.236, R.260, H.262, R.263, R.265, M.273 Ligands: MN.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.56 Hydrogen bonds: B:L.56, B:L.56, B:E.58, B:S.85, B:S.85, B:G.117, B:K.118, B:K.118, B:D.138, B:S.139, B:D.140, B:Y.233, B:R.260, B:R.260 Water bridges: B:K.118, B:D.138, B:E.236 Salt bridges: B:H.262, B:R.263, B:R.265, B:R.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Albesa-Jove, D. et al., A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase. Angew.Chem.Int.Ed.Engl. (2015)

Release Date

2015-07-15

Peptides

Glucosyl-3-phosphoglycerate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glucosyl-3-phosphoglycerate synthase

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