SMTL ID : 2v0i.1

Characterization of Substrate Binding and Catalysis of the Potential Antibacterial Target N-acetylglucosamine-1-phosphate Uridyltransferase (GlmU)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-trimer

Ligands

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

UD1.1: 21 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, Y.139, G.140, E.154, N.169, T.170, G.171, Y.197, T.199 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.197 Hydrogen bonds: A:A.12, A:A.13, A:K.25, A:K.25, A:Q.76, A:Q.76, A:G.81, A:G.140, A:E.154, A:E.154 Water bridges: A:G.14, A:E.154, A:Q.193 UD1.11: 21 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, Y.139, G.140, E.154, N.169, T.170, G.171, Y.197, T.199 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.197 Hydrogen bonds: B:A.12, B:A.13, B:K.25, B:K.25, B:Q.76, B:Q.76, B:G.81, B:G.140, B:E.154, B:E.154 Water bridges: B:G.14, B:E.154, B:Q.193 UD1.21: 21 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, Y.139, G.140, E.154, N.169, T.170, G.171, Y.197, T.199 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.197 Hydrogen bonds: C:A.12, C:A.13, C:K.25, C:K.25, C:Q.76, C:Q.76, C:G.81, C:G.140, C:E.154, C:E.154 Water bridges: C:G.14, C:E.154, C:Q.193

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

PG4.2: 2 residues within 4Å: Chain A: Y.387, P.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.387 PG4.3: 9 residues within 4Å: Chain A: F.402, T.420, G.422, A.423, I.438 Chain B: N.386, Y.387, D.388, V.410 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.423, B:D.388 PG4.12: 2 residues within 4Å: Chain B: Y.387, P.412 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.387 PG4.13: 9 residues within 4Å: Chain B: F.402, T.420, G.422, A.423, I.438 Chain C: N.386, Y.387, D.388, V.410 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.423, C:D.388 PG4.22: 2 residues within 4Å: Chain C: Y.387, P.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.387 PG4.23: 9 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410 Chain C: F.402, T.420, G.422, A.423, I.438 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.388, C:A.423

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: G.56, H.57, G.58, G.59, D.60 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.57, A:G.58, A:G.59, A:D.60, A:D.60 Water bridges: A:L.61 PEG.14: 5 residues within 4Å: Chain B: G.56, H.57, G.58, G.59, D.60 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.57, B:G.58, B:G.59, B:D.60, B:D.60 Water bridges: B:L.61 PEG.24: 5 residues within 4Å: Chain C: G.56, H.57, G.58, G.59, D.60 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.57, C:G.58, C:G.59, C:D.60, C:D.60 Water bridges: C:L.61

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

SO4.5: 4 residues within 4Å: Chain A: K.360, N.362, H.363 Chain B: K.392 Ligand excluded by PLIP SO4.6: 4 residues within 4Å: Chain A: K.360, N.377 Chain B: D.388 Chain C: R.451 Ligand excluded by PLIP SO4.7: 4 residues within 4Å: Chain A: G.14, K.15, G.16, T.17 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: K.4, K.121, E.123 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: R.331, R.333, P.334 Chain C: K.310 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain A: R.429, D.430 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: K.360, N.362, H.363 Chain C: K.392 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain A: R.451 Chain B: K.360, N.377 Chain C: D.388 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: G.14, K.15, G.16, T.17 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: K.4, K.121, E.123 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain A: K.310 Chain B: R.331, R.333, P.334 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: R.429, D.430 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain A: K.392 Chain C: K.360, N.362, H.363 Ligand excluded by PLIP SO4.26: 4 residues within 4Å: Chain A: D.388 Chain B: R.451 Chain C: K.360, N.377 Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: G.14, K.15, G.16, T.17 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain C: K.4, K.121, E.123 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: 2 residues within 4Å: Chain C: R.429, D.430 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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