SMTL ID : 3st8.1

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with COENZYME A, GLUCOSAMINE 1-PHOSPHATE and URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-trimer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: UD1.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.18, H2O.18 MG.2: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.6, MG.9, MG.13, MG.16, MG.20 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, B:D.423, H2O.21, H2O.62 MG.5: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.12, MG.19 No protein-ligand interaction detected (PLIP) MG.6: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.9, MG.13, MG.16, MG.20 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.423, B:D.423, C:D.423, H2O.1, H2O.21, H2O.41 MG.8: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: UD1.14 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.120, H2O.38, H2O.38 MG.9: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.6, MG.13, MG.16, MG.20 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, B:D.423, H2O.21, H2O.41 MG.12: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.5, MG.19 No protein-ligand interaction detected (PLIP) MG.13: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.6, MG.9, MG.16, MG.20 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.423, B:D.423, C:D.423, H2O.1, H2O.21, H2O.41 MG.15: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: UD1.21 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.120, H2O.58, H2O.58 MG.16: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.6, MG.9, MG.13, MG.20 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:D.423, B:D.423, A:D.423, H2O.41, H2O.62 MG.19: 5 residues within 4Å: Chain A: A.457 Chain B: A.457 Chain C: A.457 Ligands: MG.5, MG.12 No protein-ligand interaction detected (PLIP) MG.20: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.6, MG.9, MG.13, MG.16 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.423, B:D.423, A:D.423, H2O.1, H2O.21, H2O.41

3 x COA: COENZYME A(Non-covalent)

COA.3: 20 residues within 4Å: Chain A: G.396, A.397, 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: V.402, Y.404, V.427, V.443, R.445 Ligands: GP1.4 16 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C, 5 interactions with chain A Hydrogen bonds: B:R.461, C:Y.404, C:R.445, A:S.422, A:A.440, A:A.440 Water bridges: B:R.471, B:R.471, C:Y.404, A:A.457 Salt bridges: B:R.461, B:K.470, B:K.470 Hydrophobic interactions: C:V.402, A:L.453 pi-Cation interactions: C:R.445 COA.10: 20 residues within 4Å: Chain A: V.402, Y.404, V.427, V.443, R.445 Chain B: G.396, A.397, 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 Ligands: GP1.11 16 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: A:V.402, B:L.453 Hydrogen bonds: A:Y.404, A:R.445, B:S.422, B:A.440, B:A.440, C:R.461 Water bridges: A:Y.404, B:A.457, C:R.471, C:R.471 pi-Cation interactions: A:R.445 Salt bridges: C:R.461, C:K.470, C:K.470 COA.17: 20 residues within 4Å: Chain A: R.461, I.463, W.466, K.470, R.471 Chain B: V.402, Y.404, V.427, V.443, R.445 Chain C: G.396, A.397, G.421, S.422, G.439, A.440, L.453, V.455, A.457 Ligands: GP1.18 16 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: B:V.402, C:L.453 Hydrogen bonds: B:Y.404, B:R.445, C:S.422, C:A.440, C:A.440, A:R.461 Water bridges: B:Y.404, C:A.457, A:R.471, A:R.471 pi-Cation interactions: B:R.445 Salt bridges: A:R.461, A:K.470, A:K.470

3 x GP1: 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GP1.4: 10 residues within 4Å: Chain A: P.379, H.380, N.394 Chain C: R.350, K.368, Y.383, N.403, Y.404, K.409 Ligands: COA.3 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:Y.383, C:Y.383, C:N.403, C:N.403, C:K.409, A:N.394, A:N.394 Water bridges: C:R.350, C:K.368, C:K.409, A:K.377 Salt bridges: C:R.350, C:K.368, C:K.368, C:K.409, C:K.409, A:H.380, A:H.380 GP1.11: 10 residues within 4Å: Chain A: R.350, K.368, Y.383, N.403, Y.404, K.409 Chain B: P.379, H.380, N.394 Ligands: COA.10 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Y.383, A:Y.383, A:N.403, A:N.403, A:K.409, B:N.394, B:N.394 Water bridges: A:R.350, A:K.368, A:K.409, B:K.377 Salt bridges: A:R.350, A:K.368, A:K.368, A:K.409, A:K.409, B:H.380, B:H.380 GP1.18: 10 residues within 4Å: Chain B: R.350, K.368, Y.383, N.403, Y.404, K.409 Chain C: P.379, H.380, N.394 Ligands: COA.17 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Y.383, B:Y.383, B:N.403, B:N.403, B:K.409, C:N.394, C:N.394 Water bridges: B:R.350, B:K.368, B:K.409, C:K.377 Salt bridges: B:R.350, B:K.368, B:K.368, B:K.409, B:K.409, C:H.380, C:H.380

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

UD1.7: 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 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.95, 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:R.25, A:K.32, A:S.118, A:S.118, A:E.172, A:Q.211, A:Q.211 Salt bridges: A:K.32 UD1.14: 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.8 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:T.95, 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:R.25, B:K.32, B:S.118, B:S.118, B:E.172, B:Q.211, B:Q.211 Salt bridges: B:K.32 UD1.21: 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.15 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:T.95, 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:R.25, C:K.32, C:S.118, C:S.118, C:E.172, C:Q.211, C:Q.211 Salt bridges: 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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