SMTL ID : 2v0k.1

CHARACTERIZATION OF SUBSTRATE BINDING AND CATALYSIS OF THE POTENTIAL ANTIBACTERIAL TARGET N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE (GLMU)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 15 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, N.227 Ligands: SO4.10 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:A.12, A:A.13, A:K.25, A:K.25, A:Q.76, A:Q.76, A:G.81 Water bridges: A:G.14, A:T.82, A:T.82, A:E.195 Salt bridges: A:K.25 UDP.12: 15 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, N.227 Ligands: SO4.21 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.12, B:A.13, B:K.25, B:K.25, B:Q.76, B:Q.76, B:G.81 Water bridges: B:G.14, B:T.82, B:T.82, B:E.195 Salt bridges: B:K.25 UDP.23: 15 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, K.25, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, N.227 Ligands: SO4.32 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:A.12, C:A.13, C:K.25, C:K.25, C:Q.76, C:Q.76, C:G.81 Water bridges: C:G.14, C:T.82, C:T.82, C:E.195 Salt bridges: C:K.25

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 8 residues within 4Å: Chain A: F.402, T.420, G.422, A.423 Chain B: N.386, Y.387, D.388, V.410 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.388, A:A.423 Water bridges: A:T.439 PG4.13: 8 residues within 4Å: Chain B: F.402, T.420, G.422, A.423 Chain C: N.386, Y.387, D.388, V.410 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.423, C:D.388 Water bridges: B:T.439 PG4.24: 8 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410 Chain C: F.402, T.420, G.422, A.423 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.423, A:D.388 Water bridges: C:T.439

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 4 residues within 4Å: Chain A: V.153, D.157, N.159, Q.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.162 PGE.4: 5 residues within 4Å: Chain A: E.49, N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.49, A:N.72 Water bridges: A:I.51, A:N.72 PGE.14: 4 residues within 4Å: Chain B: V.153, D.157, N.159, Q.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.162 PGE.15: 5 residues within 4Å: Chain B: E.49, N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.49, B:N.72 Water bridges: B:I.51, B:N.72 PGE.25: 4 residues within 4Å: Chain C: V.153, D.157, N.159, Q.162 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.162 PGE.26: 5 residues within 4Å: Chain C: E.49, N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.49, C:N.72 Water bridges: C:I.51, C:N.72

21 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: K.360, N.362, H.363 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: N.377 Chain B: D.388 Chain C: R.451 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: R.331, R.333, P.334 Chain C: K.310 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: K.15, H.57, G.58 Ligand excluded by PLIP SO4.9: 3 residues within 4Å: Chain A: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: G.14, K.15, G.16, T.17, K.25 Ligands: UDP.1 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.18, N.227, Q.231 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain B: K.360, N.362, H.363 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain A: R.451 Chain B: N.377 Chain C: D.388 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain A: K.310 Chain B: R.331, R.333, P.334 Ligand excluded by PLIP SO4.19: 3 residues within 4Å: Chain B: K.15, H.57, G.58 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain B: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.21: 6 residues within 4Å: Chain B: G.14, K.15, G.16, T.17, K.25 Ligands: UDP.12 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: R.18, N.227, Q.231 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: K.360, N.362, H.363 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain A: D.388 Chain B: R.451 Chain C: N.377 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain B: K.310 Chain C: R.331, R.333, P.334 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain C: K.15, H.57, G.58 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain C: G.14, K.15, G.16, T.17, K.25 Ligands: UDP.23 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: R.18, N.227, Q.231 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mochalkin, I. et al., Characterization of Substrate Binding and Catalysis in the Potential Antibacterial Target N-Acetylglucosamine-1-Phosphate Uridyltransferase (Glmu). Protein Sci. (2007)

Release Date

2008-01-15

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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