SMTL ID : 3spt.1

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with ACETYL COENZYME A and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-trimer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: UD1.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.9, H2O.9 MG.2: 6 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: S.398, D.423 Ligands: MG.7, MG.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.423, B:D.423, H2O.1, H2O.9, H2O.17 MG.4: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.9, MG.14 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: UD1.10 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.120, H2O.17, H2O.17 MG.7: 6 residues within 4Å: Chain A: S.398, D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.12 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, H2O.1, H2O.9, H2O.17 MG.9: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.4, MG.14 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: UD1.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.120, H2O.25, H2O.25 MG.12: 6 residues within 4Å: Chain A: D.423 Chain B: S.398, D.423 Chain C: D.423 Ligands: MG.2, MG.7 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.423, B:D.423, H2O.1, H2O.9, H2O.17 MG.14: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.4, MG.9 No protein-ligand interaction detected (PLIP)

3 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.3: 23 residues within 4Å: Chain A: G.396, A.397, T.420, G.421, S.422, G.439, A.440, L.453, V.455, A.457 Chain B: R.461, I.463, W.466, K.470, R.471 Chain C: Y.383, V.400, V.402, N.403, Y.404, V.427, V.443, R.445 16 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: C:V.402, A:A.397, A:L.453 Hydrogen bonds: C:Y.404, C:R.445, A:S.422, A:S.422, A:A.440, A:A.440, B:R.461 pi-Cation interactions: C:R.445 Water bridges: B:R.471, B:R.471 Salt bridges: B:R.461, B:K.470, B:K.470 ACO.8: 23 residues within 4Å: Chain A: Y.383, V.400, V.402, N.403, Y.404, V.427, V.443, R.445 Chain B: G.396, A.397, T.420, G.421, S.422, G.439, A.440, L.453, V.455, A.457 Chain C: R.461, I.463, W.466, K.470, R.471 16 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: A:V.402, B:A.397, B:L.453 Hydrogen bonds: A:Y.404, A:R.445, C:R.461, B:S.422, B:S.422, B:A.440, B:A.440 pi-Cation interactions: A:R.445 Water bridges: C:R.471, C:R.471 Salt bridges: C:R.461, C:K.470, C:K.470 ACO.13: 23 residues within 4Å: Chain A: R.461, I.463, W.466, K.470, R.471 Chain B: Y.383, V.400, V.402, N.403, Y.404, V.427, V.443, R.445 Chain C: G.396, A.397, T.420, G.421, S.422, G.439, A.440, L.453, V.455, A.457 16 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:A.397, C:L.453, B:V.402 Hydrogen bonds: C:S.422, C:S.422, C:A.440, C:A.440, A:R.461, B:Y.404, B:R.445 Water bridges: A:R.471, A:R.471 Salt bridges: A:R.461, A:K.470, A:K.470 pi-Cation interactions: B:R.445

3 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.5: 23 residues within 4Å: Chain A: L.18, A.19, A.20, G.21, R.25, K.32, Q.89, P.92, L.93, G.94, T.95, A.98, S.118, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, N.245 Ligands: MG.1 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:E.172, A:Y.215 Hydrogen bonds: A:A.19, A:A.20, A:G.21, A:R.25, A:Q.89, A:Q.89, A:G.94, A:G.157, A:E.172, A:E.172, A:N.187, A:N.187, A:A.188, A:N.245 Water bridges: A:S.118, A:S.118, A:Q.211 Salt bridges: A:R.25, A:K.32 UD1.10: 23 residues within 4Å: Chain B: L.18, A.19, A.20, G.21, R.25, K.32, Q.89, P.92, L.93, G.94, T.95, A.98, S.118, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, N.245 Ligands: MG.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:E.172, B:Y.215 Hydrogen bonds: B:A.19, B:A.20, B:G.21, B:R.25, B:Q.89, B:Q.89, B:G.94, B:G.157, B:E.172, B:E.172, B:N.187, B:N.187, B:A.188, B:N.245 Water bridges: B:S.118, B:S.118, B:Q.211 Salt bridges: B:R.25, B:K.32 UD1.15: 23 residues within 4Å: Chain C: L.18, A.19, A.20, G.21, R.25, K.32, Q.89, P.92, L.93, G.94, T.95, A.98, S.118, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, N.245 Ligands: MG.11 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:E.172, C:Y.215 Hydrogen bonds: C:A.19, C:A.20, C:G.21, C:R.25, C:Q.89, C:Q.89, C:G.94, C:G.157, C:E.172, C:E.172, C:N.187, C:N.187, C:A.188, C:N.245 Water bridges: C:S.118, C:S.118, C:Q.211 Salt bridges: C:R.25, C:K.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jagtap, P.A. et al., Structure of Mycobacterium tuberculosis GlmU in complex with Acetyl CoA. to be published

Release Date

2012-08-08

Peptides

Bifunctional protein glmU: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bifunctional protein glmU

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