SMTL ID : 4hcq.1

Crystal structure of GLMU from mycobacterium tuberculosis in complex with glucosamine-1-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

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

GN1.1: 7 residues within 4Å: Chain A: R.350, K.368, Y.383, N.403 Chain B: P.379, H.380, N.394 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.383, A:N.403, B:H.380, B:N.394, B:N.394 Water bridges: A:R.350 Salt bridges: A:R.350, A:K.368, A:K.368, B:H.380 GN1.2: 10 residues within 4Å: Chain A: T.95, Y.156, G.157, E.172, N.187, A.188, G.189, Y.215, T.217 Ligands: MG.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.95, A:T.217 Hydrogen bonds: A:G.157, A:G.157, A:E.172, A:E.172, A:N.187, A:A.188 Water bridges: A:T.95, A:N.245, A:N.245 GN1.6: 7 residues within 4Å: Chain B: R.350, K.368, Y.383, N.403 Chain C: P.379, H.380, N.394 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Y.383, B:N.403, C:H.380, C:N.394, C:N.394 Water bridges: B:R.350 Salt bridges: B:R.350, B:K.368, B:K.368, C:H.380 GN1.7: 10 residues within 4Å: Chain B: T.95, Y.156, G.157, E.172, N.187, A.188, G.189, Y.215, T.217 Ligands: MG.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.95, B:T.217 Hydrogen bonds: B:G.157, B:G.157, B:E.172, B:E.172, B:N.187, B:A.188 Water bridges: B:T.95, B:N.245, B:N.245 GN1.11: 7 residues within 4Å: Chain A: P.379, H.380, N.394 Chain C: R.350, K.368, Y.383, N.403 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.383, C:N.403, A:H.380, A:N.394, A:N.394 Water bridges: C:R.350 Salt bridges: C:R.350, C:K.368, C:K.368, A:H.380 GN1.12: 10 residues within 4Å: Chain C: T.95, Y.156, G.157, E.172, N.187, A.188, G.189, Y.215, T.217 Ligands: MG.15 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.95, C:T.217 Hydrogen bonds: C:G.157, C:G.157, C:E.172, C:E.172, C:N.187, C:A.188 Water bridges: C:T.95, C:N.245, C:N.245

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

CO.3: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.4, CO.8, MG.9, CO.13, MG.14 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 interactions with chain A Metal complexes: C:D.423, B:D.423, B:D.423, A:D.423, A:D.423 CO.8: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.3, MG.4, MG.9, CO.13, MG.14 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 interactions with chain A Metal complexes: C:D.423, C:D.423, B:D.423, B:D.423, A:D.423 CO.13: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.3, MG.4, CO.8, MG.9, MG.14 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Metal complexes: C:D.423, C:D.423, B:D.423, A:D.423, A:D.423

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 10 residues within 4Å: Chain A: S.398, D.423 Chain B: S.398, D.423 Chain C: D.423 Ligands: CO.3, CO.8, MG.9, CO.13, MG.14 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.4, H2O.7, H2O.11 MG.5: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: GN1.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.120, H2O.1, H2O.1, H2O.1 MG.9: 10 residues within 4Å: Chain A: D.423 Chain B: S.398, D.423 Chain C: S.398, D.423 Ligands: CO.3, MG.4, CO.8, CO.13, MG.14 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.423, A:D.423, H2O.4, H2O.7, H2O.11 MG.10: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: GN1.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.120, H2O.4, H2O.4, H2O.4 MG.14: 10 residues within 4Å: Chain A: S.398, D.423 Chain B: D.423 Chain C: S.398, D.423 Ligands: CO.3, MG.4, CO.8, MG.9, CO.13 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.4, H2O.7, H2O.11 MG.15: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: GN1.12 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.120, H2O.7, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jagtap, P.K.A. et al., Crystal structures identify an atypical two-metal-ion mechanism for uridyltransfer in GlmU: its significance to sugar nucleotidyl transferases. J.Mol.Biol. (2013)

Release Date

2013-03-13

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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