SMTL ID : 4y7f.1

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate-glucose (UDP-Glc) and 3-(phosphonooxy)propanoic acid (PPA) - GpgS Mn2+ UDP-Glc PPA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.23 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.6: 3 residues within 4Å: Chain B: D.140, H.262 Ligands: UPG.8 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.140, B:H.262, H2O.2, H2O.2

2 x 48X: 3-(phosphonooxy)propanoic acid(Non-covalent)

48X.2: 9 residues within 4Å: Chain A: G.187, G.188, R.189, V.190, T.191, L.213, H.262, N.264 Ligands: UPG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.187, A:G.188, A:R.189, A:V.190, A:T.191 Salt bridges: A:R.189, A:H.262 48X.7: 9 residues within 4Å: Chain B: G.187, G.188, R.189, V.190, T.191, L.213, H.262, N.264 Ligands: UPG.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.187, B:G.188, B:R.189, B:V.190, B:T.191 Salt bridges: B:R.189, B:H.262

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

UPG.3: 21 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, 48X.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.233 Hydrogen bonds: A:L.56, A:L.56, A:E.58, 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:E.236, A:R.260, A:R.260 Water bridges: A:K.118, A:E.236 Salt bridges: A:H.262, A:R.263, A:R.265, A:R.265 UPG.8: 21 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.6, 48X.7 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.233 Hydrogen bonds: B:L.56, B:L.56, B:E.58, 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:E.236, B:R.260, B:R.260 Water bridges: B:K.118, B:E.236 Salt bridges: B:H.262, B:R.263, B:R.265, B:R.265

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: T.28, T.29, W.30, H.31 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.28, A:W.30, A:H.31 Salt bridges: A:H.31 SO4.9: 4 residues within 4Å: Chain B: T.28, T.29, W.30, H.31 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.28, B:W.30, B:H.31 Salt bridges: B:H.31

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 9 residues within 4Å: Chain A: A.230, P.231, Q.276, T.280, S.283, R.284, S.315, L.316, D.318 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.280, A:S.283, A:R.284 EDO.10: 9 residues within 4Å: Chain B: A.230, P.231, Q.276, T.280, S.283, R.284, S.315, L.316, D.318 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.280, B:S.283, B:R.284

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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