SMTL ID : 4dec.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

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

UDP.1: 14 residues within 4Å: Chain A: P.70, A.71, L.72, E.74, S.101, G.133, K.134, D.154, S.155, D.156, Y.249, R.279, R.281 Ligands: MN.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.72 Hydrogen bonds: A:L.72, A:L.72, A:E.74, A:E.74, A:S.101, A:S.101, A:G.133, A:S.155, A:D.156, A:Y.249 Water bridges: A:K.134, A:H.278, A:H.278, A:R.281 Salt bridges: A:R.281, A:R.281 UDP.7: 14 residues within 4Å: Chain B: P.70, A.71, L.72, E.74, S.101, G.133, K.134, D.154, S.155, D.156, Y.249, R.279, R.281 Ligands: MN.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.72 Hydrogen bonds: B:L.72, B:L.72, B:E.74, B:E.74, B:S.101, B:S.101, B:G.133, B:S.155, B:D.156, B:Y.249 Water bridges: B:K.134, B:H.278, B:H.278, B:R.281 Salt bridges: B:R.281, B:R.281

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

MN.2: 3 residues within 4Å: Chain A: D.156, H.278 Ligands: UDP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.156, A:H.278, H2O.1 MN.8: 3 residues within 4Å: Chain B: D.156, H.278 Ligands: UDP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.156, B:H.278, H2O.9

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

3PG.3: 6 residues within 4Å: Chain A: G.204, R.205, V.206, T.207, L.229, N.280 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.203, A:G.204, A:R.205, A:V.206, A:T.207, A:T.207 Water bridges: A:R.276 Salt bridges: A:R.205, A:H.278 3PG.9: 6 residues within 4Å: Chain B: G.204, R.205, V.206, T.207, L.229, N.280 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.203, B:G.204, B:R.205, B:V.206, B:T.207, B:T.207 Water bridges: B:R.276 Salt bridges: B:R.205, B:H.278

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 4 residues within 4Å: Chain A: Q.179, E.238, L.239, R.262 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.179, A:Q.179 Salt bridges: A:R.262 PO4.6: 4 residues within 4Å: Chain A: T.44, T.45, W.46, H.47 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.46, A:H.47, A:H.47 Salt bridges: A:H.47 PO4.10: 4 residues within 4Å: Chain B: Q.179, E.238, L.239, R.262 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.179, B:Q.179 Salt bridges: B:R.262 PO4.12: 4 residues within 4Å: Chain B: T.44, T.45, W.46, H.47 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.46, B:H.47, B:H.47 Salt bridges: B:H.47

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: R.117, V.118, V.119, Q.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.117, A:R.117 Water bridges: A:V.118, A:V.118 GOL.11: 4 residues within 4Å: Chain B: R.117, V.118, V.119, Q.123 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.117, B:R.117 Water bridges: B:V.118, B:V.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Urresti, S. et al., Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria. J.Biol.Chem. (2012)

Release Date

2012-06-06

Peptides

GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS)

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