SMTL ID : 4g3p.1

Crystal structure of GlmU from Mycobacterium tuberculosis Snapshot 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 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.4, UD1.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.23, A:T.24, A:T.24, A:R.25 Water bridges: A:K.32, A:Q.211, A:E.213, A:N.245 Salt bridges: A:R.25, A:R.25, A:K.32 POP.7: 6 residues within 4Å: Chain B: P.22, G.23, T.24, R.25 Ligands: MG.10, UD1.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.23, B:T.24, B:T.24, B:R.25 Water bridges: B:K.32, B:Q.211, B:E.213, B:N.245 Salt bridges: B:R.25, B:R.25, B:K.32 POP.13: 6 residues within 4Å: Chain C: P.22, G.23, T.24, R.25 Ligands: MG.16, UD1.18 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.23, C:T.24, C:T.24, C:R.25 Water bridges: C:K.32, C:Q.211, C:E.213, C:N.245 Salt bridges: C:R.25, C:R.25, C:K.32

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: CO.5, MG.8, CO.11, MG.14, CO.17 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.7, H2O.14, H2O.22 MG.4: 3 residues within 4Å: Chain A: R.25, Q.211 Ligands: POP.1 No protein-ligand interaction detected (PLIP) MG.8: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, CO.5, CO.11, MG.14, CO.17 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.7, H2O.14, H2O.22 MG.10: 3 residues within 4Å: Chain B: R.25, Q.211 Ligands: POP.7 No protein-ligand interaction detected (PLIP) MG.14: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, CO.5, MG.8, CO.11, CO.17 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:D.423, A:D.423, B:D.423, H2O.7, H2O.14, H2O.22 MG.16: 3 residues within 4Å: Chain C: R.25, Q.211 Ligands: POP.13 No protein-ligand interaction detected (PLIP)

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

CO.3: 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.6, H2O.6 CO.5: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, MG.8, CO.11, MG.14, CO.17 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.423, A:D.423, B:D.423 CO.9: 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.14, H2O.14 CO.11: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, CO.5, MG.8, MG.14, CO.17 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: C:D.423, A:D.423, B:D.423 CO.15: 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.22, H2O.22 CO.17: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.2, CO.5, MG.8, CO.11, MG.14 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:D.423, A:D.423, C:D.423

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

UD1.6: 25 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, N.245 Ligands: POP.1, CO.3 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:E.172, A:Y.215, A:T.217 Hydrogen bonds: 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:A.188, A:N.245 Water bridges: A:R.25, A:S.118, A:S.118, A:E.172, A:Q.211, A:Q.211 Salt bridges: A:R.25, A:K.32 UD1.12: 25 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, N.245 Ligands: POP.7, CO.9 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:E.172, B:Y.215, B:T.217 Hydrogen bonds: 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:A.188, B:N.245 Water bridges: B:R.25, B:S.118, B:S.118, B:E.172, B:Q.211, B:Q.211 Salt bridges: B:R.25, B:K.32 UD1.18: 25 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, N.245 Ligands: POP.13, CO.15 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:E.172, C:Y.215, C:T.217 Hydrogen bonds: 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:A.188, C:N.245 Water bridges: C:R.25, C:S.118, C:S.118, C:E.172, C:Q.211, 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., 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

Related Entries With Identical Sequence