SMTL ID : 4y9x.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.64 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: D.140, H.262, R.263 Ligands: UPG.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.140, A:H.262, H2O.1, H2O.2 MN.8: 4 residues within 4Å: Chain B: D.140, H.262, R.263 Ligands: UPG.11 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.140, B:H.262, H2O.3, H2O.4

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

CL.2: 2 residues within 4Å: Chain A: R.246, K.323 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.246, K.323 Ligand excluded by PLIP

2 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.3: 8 residues within 4Å: Chain A: G.187, G.188, R.189, V.190, T.191, H.262, N.264 Ligands: UPG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.188, A:R.189, A:V.190, A:T.191 Water bridges: A:R.260, A:H.262 Salt bridges: A:R.189, A:H.262 3PG.10: 8 residues within 4Å: Chain B: G.187, G.188, R.189, V.190, T.191, H.262, N.264 Ligands: UPG.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.188, B:R.189, B:V.190, B:T.191 Water bridges: B:R.260, B:H.262 Salt bridges: B:R.189, B:H.262

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

UPG.4: 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, 3PG.3 24 PLIP interactions: 24 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:S.139, A:D.140, A:Y.233, A:Y.233, A:E.236, A:R.260, A:R.260, A:R.265 Water bridges: A:K.118, A:E.236 Salt bridges: A:H.262, A:R.263, A:R.265 UPG.11: 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.8, 3PG.10 24 PLIP interactions: 24 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:S.139, B:D.140, B:Y.233, B:Y.233, B:E.236, B:R.260, B:R.260, B:R.265 Water bridges: B:K.118, B:E.236 Salt bridges: B:H.262, B:R.263, B:R.265

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

EDO.5: 3 residues within 4Å: Chain A: R.105, V.114, P.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.105, A:V.114 EDO.6: 8 residues within 4Å: Chain A: A.230, P.231, T.280, S.283, R.284, S.315, L.316, D.318 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.280, A:S.283, A:S.283, A:R.284 EDO.7: 5 residues within 4Å: Chain A: R.47, L.156, G.159, E.160, G.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.47 EDO.12: 3 residues within 4Å: Chain B: R.105, V.114, P.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.105, B:V.114 EDO.13: 8 residues within 4Å: Chain B: A.230, P.231, T.280, S.283, R.284, S.315, L.316, D.318 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.280, B:S.283, B:S.283, B:R.284 EDO.14: 5 residues within 4Å: Chain B: R.47, L.156, G.159, E.160, G.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.47

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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