SMTL ID : 4g3q.1

Crystal structure of GlmU from Mycobacterium tuberculosis Snapshot 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

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

POP.1: 6 residues within 4Å: Chain A: P.22, G.23, T.24, R.25 Ligands: MG.2, UD1.6 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:K.32, A:K.32, A:E.213, A:E.213 Salt bridges: A:R.25, A:K.32 POP.7: 6 residues within 4Å: Chain B: P.22, G.23, T.24, R.25 Ligands: MG.8, UD1.12 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:K.32, B:K.32, B:E.213, B:E.213 Salt bridges: B:R.25, B:K.32 POP.13: 6 residues within 4Å: Chain C: P.22, G.23, T.24, R.25 Ligands: MG.14, UD1.18 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:K.32, C:K.32, C:E.213, C:E.213 Salt bridges: C:R.25, C:K.32

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: POP.1 No protein-ligand interaction detected (PLIP) MG.3: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.5, MG.9, CO.11, MG.15, CO.17 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, B:D.423, H2O.1, H2O.21, H2O.42 MG.8: 1 residues within 4Å: Ligands: POP.7 No protein-ligand interaction detected (PLIP) MG.9: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.3, CO.5, CO.11, MG.15, CO.17 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, B:D.423, H2O.1, H2O.21, H2O.42 MG.14: 1 residues within 4Å: Ligands: POP.13 No protein-ligand interaction detected (PLIP) MG.15: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.3, CO.5, MG.9, CO.11, CO.17 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.423, C:D.423, B:D.423, H2O.1, H2O.21, H2O.42

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

CO.4: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: UD1.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.21, H2O.21 CO.5: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.3, MG.9, CO.11, MG.15, CO.17 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.423, A:D.423, C:D.423, C:D.423, B:D.423 CO.10: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: UD1.12 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.120, H2O.42, H2O.42 CO.11: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.3, CO.5, MG.9, MG.15, CO.17 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Metal complexes: A:D.423, A:D.423, C:D.423, B:D.423, B:D.423 CO.16: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: UD1.18 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.120, H2O.63, H2O.63 CO.17: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.3, CO.5, MG.9, CO.11, MG.15 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Metal complexes: A:D.423, A:D.423, B:D.423, C:D.423, C:D.423

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

UD1.6: 26 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, G.119, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: POP.1, CO.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.215 Hydrogen bonds: A:A.20, A:G.21, A:R.25, A:Q.89, A:Q.89, A:G.94, A:T.95, A:G.119, A:D.120, A:G.157, A:E.172, A:E.172, A:N.187, A:A.188 Water bridges: A:R.25, A:K.32, A:K.32, A:S.118, A:S.118, A:Q.211, A:Q.211, A:N.245 Salt bridges: A:R.25, A:K.32 UD1.12: 26 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, G.119, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: POP.7, CO.10 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.215 Hydrogen bonds: B:A.20, B:G.21, B:R.25, B:Q.89, B:Q.89, B:G.94, B:T.95, B:G.119, B:D.120, B:G.157, B:E.172, B:E.172, B:N.187, B:A.188 Water bridges: B:R.25, B:K.32, B:K.32, B:S.118, B:S.118, B:Q.211, B:Q.211, B:N.245 Salt bridges: B:R.25, B:K.32 UD1.18: 26 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, G.119, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: POP.13, CO.16 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:Y.215 Hydrogen bonds: C:A.20, C:G.21, C:R.25, C:Q.89, C:Q.89, C:G.94, C:T.95, C:G.119, C:D.120, C:G.157, C:E.172, C:E.172, C:N.187, C:A.188 Water bridges: C:R.25, C:K.32, C:K.32, C:S.118, C:S.118, C:Q.211, C:Q.211, C:N.245 Salt bridges: C:R.25, C:K.32

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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