SMTL ID : 5jt0.1

Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgS*GPG*UDP*Mn2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 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: UDP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.140, A:H.262, H2O.1 MN.6: 4 residues within 4Å: Chain B: D.140, H.262, R.263 Ligands: UDP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.140, B:H.262, H2O.2

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

UDP.2: 18 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, Y.233, R.260, H.262, R.263, R.265, M.273 Ligands: MN.1, XDX.5 16 PLIP interactions: 16 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:S.139, A:D.140, A:R.260, A:R.263, A:R.265 Water bridges: A:D.138 Salt bridges: A:H.262, A:R.263, A:R.265 UDP.7: 18 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, Y.233, R.260, H.262, R.263, R.265, M.273 Ligands: MN.6, XDX.10 16 PLIP interactions: 16 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:S.139, B:D.140, B:R.260, B:R.263, B:R.265 Water bridges: B:D.138 Salt bridges: B:H.262, B:R.263, B:R.265

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

EDO.3: 9 residues within 4Å: Chain A: A.230, P.231, Q.276, 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.4: 2 residues within 4Å: Chain A: R.105, P.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.105, A:R.105 EDO.8: 9 residues within 4Å: Chain B: A.230, P.231, Q.276, 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.9: 2 residues within 4Å: Chain B: R.105, P.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.105, B:R.105

2 x XDX: (2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid(Non-covalent)

XDX.5: 18 residues within 4Å: Chain A: K.118, D.138, Y.169, G.187, G.188, R.189, V.190, T.191, L.213, S.214, G.215, Y.233, E.236, R.260, H.262, N.264, M.273 Ligands: UDP.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:K.118, A:D.138, A:Y.169, A:G.187, A:G.188, A:R.189, A:V.190, A:T.191, A:T.191, A:G.215, A:Y.233, A:R.260, A:R.260, A:N.264, A:R.265 Water bridges: A:Y.169, A:Q.211 Salt bridges: A:R.189, A:H.262 XDX.10: 18 residues within 4Å: Chain B: K.118, D.138, Y.169, G.187, G.188, R.189, V.190, T.191, L.213, S.214, G.215, Y.233, E.236, R.260, H.262, N.264, M.273 Ligands: UDP.7 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.118, B:D.138, B:Y.169, B:G.187, B:G.188, B:R.189, B:V.190, B:T.191, B:T.191, B:G.215, B:Y.233, B:R.260, B:R.260, B:N.264, B:R.265 Water bridges: B:Y.169, B:Q.211 Salt bridges: B:R.189, B:H.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Albesa-Jove, D. et al., Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS. Structure (2017)

Release Date

2017-05-24

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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