SMTL ID : 2v0h.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 1.79 Å

Oligo State

homo-trimer

Ligands

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

PEG.1: 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 PEG.2: 4 residues within 4Å: Chain A: N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.49, A:I.51, A:Q.70, A:N.72 PEG.3: 5 residues within 4Å: Chain A: V.131, Y.139, N.169, T.170, E.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.224 Water bridges: A:G.225 PEG.4: 7 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410 Chain C: F.402, G.422, A.423 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:A.423, A:D.388 Water bridges: C:T.439, C:T.439 PEG.12: 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 PEG.13: 4 residues within 4Å: Chain B: N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.49, B:I.51, B:Q.70, B:N.72 PEG.14: 5 residues within 4Å: Chain B: V.131, Y.139, N.169, T.170, E.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.224 Water bridges: B:G.225 PEG.15: 7 residues within 4Å: Chain A: F.402, G.422, A.423 Chain B: N.386, Y.387, D.388, V.410 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.388, A:A.423 Water bridges: A:T.439, A:T.439 PEG.23: 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 PEG.24: 4 residues within 4Å: Chain C: N.50, Q.70, V.71, N.72 4 PLIP interactions: 4 interactions with chain C Water bridges: C:E.49, C:I.51, C:Q.70, C:N.72 PEG.25: 5 residues within 4Å: Chain C: V.131, Y.139, N.169, T.170, E.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.224 Water bridges: C:G.225 PEG.26: 7 residues within 4Å: Chain B: F.402, G.422, A.423 Chain C: N.386, Y.387, D.388, V.410 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:D.388, B:A.423 Water bridges: B:T.439, B:T.439

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

SO4.5: 4 residues within 4Å: Chain A: N.377, F.402 Chain B: D.388 Chain C: R.451 8 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:D.388, A:N.377 Water bridges: A:K.360, C:R.451, C:R.451, C:R.451 Salt bridges: A:K.360, C:R.451 SO4.6: 4 residues within 4Å: Chain A: K.360, N.362, H.363 Chain B: K.392 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.362 Water bridges: A:H.363, A:N.377, A:N.377, A:N.377, B:Y.366, B:Y.366 Salt bridges: A:K.360, A:H.363, B:K.392 SO4.7: 4 residues within 4Å: Chain A: R.331, R.333, P.334 Chain C: K.310 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain C Water bridges: A:R.331, A:R.331, A:R.331, A:R.331, C:K.310, C:K.310, C:K.310, C:K.310 Salt bridges: A:R.331, A:R.333, C:K.310 SO4.8: 3 residues within 4Å: Chain A: H.57, E.78, Q.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.79, A:Q.79 Salt bridges: A:H.57 SO4.9: 3 residues within 4Å: Chain A: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.58 Water bridges: A:G.59 Salt bridges: A:K.15, A:H.57 SO4.16: 4 residues within 4Å: Chain A: R.451 Chain B: N.377, F.402 Chain C: D.388 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:N.377, C:D.388 Water bridges: B:K.360, A:R.451, A:R.451, A:R.451 Salt bridges: B:K.360, A:R.451 SO4.17: 4 residues within 4Å: Chain B: K.360, N.362, H.363 Chain C: K.392 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.362 Water bridges: B:H.363, B:N.377, B:N.377, B:N.377, C:Y.366, C:Y.366 Salt bridges: B:K.360, B:H.363, C:K.392 SO4.18: 4 residues within 4Å: Chain A: K.310 Chain B: R.331, R.333, P.334 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Water bridges: B:R.331, B:R.331, B:R.331, B:R.331, A:K.310, A:K.310, A:K.310, A:K.310 Salt bridges: B:R.331, B:R.333, A:K.310 SO4.19: 3 residues within 4Å: Chain B: H.57, E.78, Q.79 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.79, B:Q.79 Salt bridges: B:H.57 SO4.20: 3 residues within 4Å: Chain B: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.58 Water bridges: B:G.59 Salt bridges: B:K.15, B:H.57 SO4.27: 4 residues within 4Å: Chain A: D.388 Chain B: R.451 Chain C: N.377, F.402 8 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 3 interactions with chain C Water bridges: B:R.451, B:R.451, B:R.451, C:K.360 Salt bridges: B:R.451, C:K.360 Hydrogen bonds: A:D.388, C:N.377 SO4.28: 4 residues within 4Å: Chain A: K.392 Chain C: K.360, N.362, H.363 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:N.362 Water bridges: C:H.363, C:N.377, C:N.377, C:N.377, A:Y.366, A:Y.366 Salt bridges: C:K.360, C:H.363, A:K.392 SO4.29: 4 residues within 4Å: Chain B: K.310 Chain C: R.331, R.333, P.334 11 PLIP interactions: 6 interactions with chain C, 5 interactions with chain B Water bridges: C:R.331, C:R.331, C:R.331, C:R.331, B:K.310, B:K.310, B:K.310, B:K.310 Salt bridges: C:R.331, C:R.333, B:K.310 SO4.30: 3 residues within 4Å: Chain C: H.57, E.78, Q.79 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.79, C:Q.79 Salt bridges: C:H.57 SO4.31: 3 residues within 4Å: Chain C: K.15, H.57, G.58 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.58 Water bridges: C:G.59 Salt bridges: C:K.15, C:H.57

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

CO.10: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.11, CO.21, CO.22, CO.32, CO.33 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.406, C:D.406, B:D.406, H2O.20, H2O.39, H2O.58 CO.11: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.10, CO.21, CO.22, CO.32, CO.33 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.406, C:D.406, B:D.406, H2O.20, H2O.39, H2O.58 CO.21: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.10, CO.11, CO.22, CO.32, CO.33 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.406, C:D.406, B:D.406, H2O.20, H2O.39, H2O.58 CO.22: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.10, CO.11, CO.21, CO.32, CO.33 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: A:D.406, B:D.406, C:D.406, H2O.20, H2O.39, H2O.58 CO.32: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.10, CO.11, CO.21, CO.22, CO.33 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.406, A:D.406, C:D.406, H2O.20, H2O.39, H2O.58 CO.33: 8 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: CO.10, CO.11, CO.21, CO.22, CO.32 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.406, A:D.406, C:D.406, H2O.20, H2O.39, H2O.58

Links

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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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