SMTL ID : 4g3s.1

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-n-acetylglucosamine and pyrophosphate Snapshot 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-trimer

Ligands

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

UD1.1: 24 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: POP.3, CO.6 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.215, A:T.217 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.119, A:D.120, A:G.157, A:E.172, A:E.172, A:N.187, A:N.245 Water bridges: A:R.25, A:R.25, A:S.118, A:S.118, A:T.121, A:E.172, A:A.188, A:Q.211, A:Q.211 Salt bridges: A:R.25, A:K.32 UD1.8: 24 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: POP.10, CO.13 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:Y.215, B:T.217 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.119, B:D.120, B:G.157, B:E.172, B:E.172, B:N.187, B:N.245 Water bridges: B:R.25, B:R.25, B:S.118, B:S.118, B:T.121, B:E.172, B:A.188, B:Q.211, B:Q.211 Salt bridges: B:R.25, B:K.32 UD1.15: 24 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: POP.17, CO.20 27 PLIP interactions: 27 interactions with chain C Hydrophobic interactions: C:Y.215, C:T.217 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.119, C:D.120, C:G.157, C:E.172, C:E.172, C:N.187, C:N.245 Water bridges: C:R.25, C:R.25, C:S.118, C:S.118, C:T.121, C:E.172, C:A.188, C:Q.211, C:Q.211 Salt bridges: C:R.25, C:K.32

3 x GN1: 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose(Non-covalent)

GN1.2: 8 residues within 4Å: Chain A: R.350, K.368, Y.383, V.400, N.403 Chain B: P.379, H.380, N.394 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.383, A:V.400 Hydrogen bonds: A:Y.383, A:N.403, B:H.380, B:N.394, B:N.394 Water bridges: A:R.350, A:R.350, A:R.350, B:K.377, B:H.380, B:A.397 Salt bridges: A:R.350, A:K.368, B:H.380 GN1.9: 8 residues within 4Å: Chain B: R.350, K.368, Y.383, V.400, N.403 Chain C: P.379, H.380, N.394 16 PLIP interactions: 7 interactions with chain C, 9 interactions with chain B Hydrogen bonds: C:H.380, C:N.394, C:N.394, B:Y.383, B:N.403 Water bridges: C:K.377, C:H.380, C:A.397, B:R.350, B:R.350, B:R.350 Salt bridges: C:H.380, B:R.350, B:K.368 Hydrophobic interactions: B:Y.383, B:V.400 GN1.16: 8 residues within 4Å: Chain A: P.379, H.380, N.394 Chain C: R.350, K.368, Y.383, V.400, N.403 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain C Hydrogen bonds: A:H.380, A:N.394, A:N.394, C:Y.383, C:N.403 Water bridges: A:K.377, A:H.380, A:A.397, C:R.350, C:R.350, C:R.350 Salt bridges: A:H.380, C:R.350, C:K.368 Hydrophobic interactions: C:Y.383, C:V.400

3 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.3: 8 residues within 4Å: Chain A: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: UD1.1, MG.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.23, A:T.24, A:T.24, A:R.25 Water bridges: A:G.21, A:K.32, A:K.32 Salt bridges: A:R.25, A:K.32, A:K.32 POP.10: 8 residues within 4Å: Chain B: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: UD1.8, MG.12 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.23, B:T.24, B:T.24, B:R.25 Water bridges: B:G.21, B:K.32, B:K.32 Salt bridges: B:R.25, B:K.32, B:K.32 POP.17: 8 residues within 4Å: Chain C: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: UD1.15, MG.19 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.23, C:T.24, C:T.24, C:R.25 Water bridges: C:G.21, C:K.32, C:K.32 Salt bridges: C:R.25, C:K.32, C:K.32

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 9 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: S.398, D.423 Ligands: CO.7, MG.11, CO.14, MG.18, CO.21 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, H2O.1, H2O.15, H2O.29 MG.5: 3 residues within 4Å: Chain A: R.25, Q.211 Ligands: POP.3 No protein-ligand interaction detected (PLIP) MG.11: 9 residues within 4Å: Chain A: S.398, D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.4, CO.7, CO.14, MG.18, CO.21 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.15, H2O.29 MG.12: 3 residues within 4Å: Chain B: R.25, Q.211 Ligands: POP.10 No protein-ligand interaction detected (PLIP) MG.18: 9 residues within 4Å: Chain A: D.423 Chain B: S.398, D.423 Chain C: D.423 Ligands: MG.4, CO.7, MG.11, CO.14, CO.21 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.15, H2O.29 MG.19: 3 residues within 4Å: Chain C: R.25, Q.211 Ligands: POP.17 No protein-ligand interaction detected (PLIP)

6 x CO: COBALT (II) ION(Non-covalent)

CO.6: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: UD1.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.14, H2O.14 CO.7: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.4, MG.11, CO.14, MG.18, CO.21 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.13, H2O.41 CO.13: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: UD1.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.120, H2O.29, H2O.29 CO.14: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.4, CO.7, MG.11, MG.18, CO.21 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.13, H2O.27 CO.20: 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.43, H2O.43 CO.21: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.4, CO.7, MG.11, CO.14, MG.18 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.27, H2O.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jagtap, P.A. et al., Structural Snapshots of Glmu from Mycobacterium Tuberculosis. To be Published

Release Date

2013-08-07

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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