SMTL ID : 5jsx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 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.2 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.5 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 UPG: URIDINE-5'-DIPHOSPHATE-GLUCOSE(Non-covalent)

UPG.2: 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, GOL.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:K.118 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:D.138, A:S.139, A:D.140, A:Y.233, A:Y.233, A:E.236, A:R.260, A:R.260 Water bridges: A:E.236 Salt bridges: A:H.262, A:R.263, A:R.265, A:R.265 UPG.5: 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.4, GOL.6 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:K.118 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:D.138, B:S.139, B:D.140, B:Y.233, B:Y.233, B:E.236, B:R.260, B:R.260 Water bridges: B:E.236 Salt bridges: B:H.262, B:R.263, B:R.265, B:R.265

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: Y.169, G.188, R.189, V.190, T.191, R.260, H.262 Ligands: UPG.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.169, A:Y.169, A:V.190, A:T.191, A:R.260 Water bridges: A:H.262 GOL.6: 8 residues within 4Å: Chain B: Y.169, G.188, R.189, V.190, T.191, R.260, H.262 Ligands: UPG.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.169, B:Y.169, B:V.190, B:T.191, B:R.260 Water bridges: 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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