SMTL ID : 4g87.1

Crystal structure of GLMU from Mycobacterium tuberculosis snapshot 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-trimer

Ligands

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

MG.1: 9 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: S.398, D.423 Ligands: CO.3, MG.7, CO.9, MG.13, CO.15 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.8, H2O.26 MG.4: 2 residues within 4Å: Ligands: UD1.5, POP.6 No protein-ligand interaction detected (PLIP) MG.7: 9 residues within 4Å: Chain A: S.398, D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.1, CO.3, CO.9, MG.13, CO.15 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.26, H2O.45 MG.10: 2 residues within 4Å: Ligands: UD1.11, POP.12 No protein-ligand interaction detected (PLIP) MG.13: 9 residues within 4Å: Chain A: D.423 Chain B: S.398, D.423 Chain C: D.423 Ligands: MG.1, CO.3, MG.7, CO.9, CO.15 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.8, H2O.45 MG.16: 2 residues within 4Å: Ligands: UD1.17, POP.18 No protein-ligand interaction detected (PLIP)

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

CO.2: 4 residues within 4Å: Chain A: K.32, D.120, N.245 Ligands: UD1.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.120, H2O.2, H2O.4 CO.3: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.1, MG.7, CO.9, MG.13, CO.15 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:D.423, B:D.423, A:D.423 CO.8: 4 residues within 4Å: Chain B: K.32, D.120, N.245 Ligands: UD1.11 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.120, H2O.20, H2O.22 CO.9: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.1, CO.3, MG.7, MG.13, CO.15 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:D.423, B:D.423, A:D.423 CO.14: 4 residues within 4Å: Chain C: K.32, D.120, N.245 Ligands: UD1.17 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.120, H2O.38, H2O.40 CO.15: 8 residues within 4Å: Chain A: D.423 Chain B: D.423 Chain C: D.423 Ligands: MG.1, CO.3, MG.7, CO.9, MG.13 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:D.423, B:D.423, A:D.423

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

UD1.5: 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, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: CO.2, MG.4, POP.6 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:E.172, 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:Q.211, A:Q.211, A:Q.211, A:A.242 Salt bridges: A:R.25, A:K.32 UD1.11: 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, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: CO.8, MG.10, POP.12 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:E.172, 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:Q.211, B:Q.211, B:Q.211, B:A.242 Salt bridges: B:R.25, B:K.32 UD1.17: 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, D.120, Y.156, G.157, E.172, N.187, A.188, Y.215, T.217, G.243, N.245 Ligands: CO.14, MG.16, POP.18 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:E.172, 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:D.120, C:D.120, C:T.121, C:E.172, C:Q.211, C:Q.211, C:Q.211, C:A.242 Salt bridges: C:R.25, C:K.32

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

POP.6: 8 residues within 4Å: Chain A: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: MG.4, UD1.5 9 PLIP interactions: 9 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 Salt bridges: A:R.25, A:K.32, A:K.32 POP.12: 8 residues within 4Å: Chain B: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: MG.10, UD1.11 9 PLIP interactions: 9 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 Salt bridges: B:R.25, B:K.32, B:K.32 POP.18: 8 residues within 4Å: Chain C: G.21, P.22, G.23, T.24, R.25, K.32 Ligands: MG.16, UD1.17 9 PLIP interactions: 9 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 Salt bridges: C:R.25, C:K.32, C:K.32

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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