SMTL ID : 2vd4.1

Structure of small-molecule inhibitor of Glmu from Haemophilus influenzae reveals an allosteric binding site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x P21: 4-chloro-N-(3-methoxypropyl)-N-[(3S)-1-(2-phenylethyl)piperidin-3-yl]benzamide(Non-covalent)

P21.1: 12 residues within 4Å: Chain A: Y.139, N.169, T.170, V.220, M.221, V.223, E.224, G.225, Q.231, A.234, L.235 Ligands: SO4.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.139, A:V.220, A:V.223, A:Q.231 Hydrogen bonds: A:Q.231 Salt bridges: A:E.224 P21.13: 12 residues within 4Å: Chain B: Y.139, N.169, T.170, V.220, M.221, V.223, E.224, G.225, Q.231, A.234, L.235 Ligands: SO4.17 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.139, B:V.220, B:V.223, B:Q.231 Hydrogen bonds: B:Q.231 Salt bridges: B:E.224 P21.25: 12 residues within 4Å: Chain C: Y.139, N.169, T.170, V.220, M.221, V.223, E.224, G.225, Q.231, A.234, L.235 Ligands: SO4.29 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.139, C:V.220, C:V.223, C:Q.231 Hydrogen bonds: C:Q.231 Salt bridges: C:E.224

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

SO4.2: 3 residues within 4Å: Chain A: K.360, N.362, H.363 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: K.15, H.57, G.58 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: N.377 Chain B: D.388 Chain C: R.451 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: N.227, Q.231 Ligands: P21.1 Ligand excluded by PLIP SO4.6: 3 residues within 4Å: Chain A: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.12: 4 residues within 4Å: Chain A: K.310 Chain B: R.331, R.333, P.334 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: K.360, N.362, H.363 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: K.15, H.57, G.58 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain A: R.451 Chain B: N.377 Chain C: D.388 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: N.227, Q.231 Ligands: P21.13 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.24: 4 residues within 4Å: Chain B: K.310 Chain C: R.331, R.333, P.334 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: K.360, N.362, H.363 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: K.15, H.57, G.58 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: 3 residues within 4Å: Chain C: N.227, Q.231 Ligands: P21.25 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain C: H.57, E.78, Q.79 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain A: R.331, R.333, P.334 Chain C: K.310 Ligand excluded by PLIP

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

PG4.7: 7 residues within 4Å: Chain A: E.49, N.50, I.51, Q.70, V.71, N.72, F.92 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.72 PG4.8: 9 residues within 4Å: Chain A: F.402, T.420, G.422, A.423 Chain B: N.386, Y.387, D.388, V.410, T.426 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 PG4.19: 7 residues within 4Å: Chain B: E.49, N.50, I.51, Q.70, V.71, N.72, F.92 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.72 PG4.20: 9 residues within 4Å: Chain B: F.402, T.420, G.422, A.423 Chain C: N.386, Y.387, D.388, V.410, T.426 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.423, C:D.388 Water bridges: B:T.439, B:T.439 PG4.31: 7 residues within 4Å: Chain C: E.49, N.50, I.51, Q.70, V.71, N.72, F.92 1 PLIP interactions: 1 interactions with chain C Water bridges: C:N.72 PG4.32: 9 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410, T.426 Chain C: F.402, T.420, 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

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

PGE.9: 4 residues within 4Å: Chain A: V.153, D.157, N.159, Q.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.159, A:Q.162 PGE.21: 4 residues within 4Å: Chain B: V.153, D.157, N.159, Q.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.159, B:Q.162 PGE.33: 4 residues within 4Å: Chain C: V.153, D.157, N.159, Q.162 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.159, C:Q.162

6 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.22, MG.34 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.10, H2O.21, H2O.32 MG.11: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.23, MG.35 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.9, H2O.20, H2O.32 MG.22: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.10, MG.34 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.10, H2O.21, H2O.32 MG.23: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.11, MG.35 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.9, H2O.20, H2O.32 MG.34: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.10, MG.22 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.406, B:D.406, A:D.406, H2O.10, H2O.21, H2O.32 MG.35: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.11, MG.23 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.406, B:D.406, A:D.406, H2O.9, H2O.20, H2O.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mochalkin, I. et al., Structure of a Small-Molecule Inhibitor Complexed with Glmu from Haemophilus Influenzae Reveals an Allosteric Binding Site. Protein Sci. (2008)

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

Related Entries With Identical Sequence