SMTL ID : 4kql.1

Hin GlmU bound to WG578

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-trimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.4, K.121, E.123 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.3: 4 residues within 4Å: Chain A: R.331, R.333, P.334 Chain B: K.310 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: R.333, K.351, Y.366, K.392 Chain B: H.363 Ligand excluded by PLIP SO4.5: 2 residues within 4Å: Chain A: H.57, G.58 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: N.227, Q.231 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: K.4, K.121, E.123 Ligand excluded by PLIP SO4.13: 5 residues within 4Å: Chain B: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.14: 4 residues within 4Å: Chain B: R.331, R.333, P.334 Chain C: K.310 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain B: R.333, K.351, Y.366, K.392 Chain C: H.363 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: H.57, G.58 Ligand excluded by PLIP SO4.17: 2 residues within 4Å: Chain B: N.227, Q.231 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: K.4, K.121, E.123 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: G.14, K.15, G.16, T.17, K.25 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain A: K.310 Chain C: R.331, R.333, P.334 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain A: H.363 Chain C: R.333, K.351, Y.366, K.392 Ligand excluded by PLIP SO4.27: 2 residues within 4Å: Chain C: H.57, G.58 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain C: N.227, Q.231 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.18, MG.29 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 MG.8: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.19, MG.30 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 MG.18: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.7, MG.29 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 MG.19: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.8, MG.30 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 MG.29: 5 residues within 4Å: Chain A: D.406 Chain B: D.406 Chain C: D.406 Ligands: MG.7, MG.18 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406 MG.30: 8 residues within 4Å: Chain A: D.406, Q.408 Chain B: D.406, Q.408 Chain C: D.406, Q.408 Ligands: MG.8, MG.19 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:D.406, C:D.406, A:D.406

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

PG4.9: 9 residues within 4Å: Chain A: F.402, T.420, G.422, A.423 Chain C: N.386, Y.387, D.388, V.410, T.426 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.388, A:A.423 Water bridges: C:D.388 PG4.10: 6 residues within 4Å: Chain A: N.189, N.190, N.191, A.192, Q.193, G.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:Y.196 PG4.20: 9 residues within 4Å: Chain A: N.386, Y.387, D.388, V.410, T.426 Chain B: F.402, T.420, G.422, A.423 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.423, A:D.388 Water bridges: A:D.388 PG4.21: 6 residues within 4Å: Chain B: N.189, N.190, N.191, A.192, Q.193, G.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.189 Water bridges: B:Y.196 PG4.31: 9 residues within 4Å: Chain B: N.386, Y.387, D.388, V.410, T.426 Chain C: F.402, T.420, G.422, A.423 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.388, C:A.423 Water bridges: B:D.388 PG4.32: 6 residues within 4Å: Chain C: N.189, N.190, N.191, A.192, Q.193, G.194 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.189 Water bridges: C:Y.196

3 x 1SG: N-(4-{[3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-methoxybenzoyl]amino}phenyl)pyridine-2-carboxamide(Non-covalent)

1SG.11: 21 residues within 4Å: Chain A: L.11, A.12, A.13, G.14, K.25, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.11, A:L.11, A:T.82, A:Y.103, A:Y.103, A:V.131, A:Y.139 Hydrogen bonds: A:A.13, A:G.14, A:Q.76, A:Q.76, A:G.81, A:D.105, A:T.170, A:G.225 Water bridges: A:K.25, A:Y.139 1SG.22: 21 residues within 4Å: Chain B: L.11, A.12, A.13, G.14, K.25, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.11, B:L.11, B:T.82, B:Y.103, B:Y.103, B:V.131, B:Y.139 Hydrogen bonds: B:A.13, B:G.14, B:Q.76, B:Q.76, B:G.81, B:D.105, B:T.170, B:G.225 Water bridges: B:K.25, B:Y.139 1SG.33: 21 residues within 4Å: Chain C: L.11, A.12, A.13, G.14, K.25, V.26, Q.76, Q.79, L.80, G.81, T.82, A.85, Y.103, D.105, V.131, Y.139, N.169, T.170, V.223, E.224, G.225 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.11, C:L.11, C:T.82, C:Y.103, C:Y.103, C:V.131, C:Y.139 Hydrogen bonds: C:A.13, C:G.14, C:Q.76, C:Q.76, C:G.81, C:D.105, C:T.170, C:G.225 Water bridges: C:K.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Doig, P. et al., Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping. Bioorg.Med.Chem. (2014)

Release Date

2014-10-15

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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