SMTL ID : 8pay.1

Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.21 Å

Oligo State

homo-dimer

Ligands

2 x ACE- GLN- ALC- LV8- LEU- PHE: ACE-GLN-ALC-GLC-LEU-PHE(Non-covalent)

ACE-GLN-ALC-LV8-LEU-PHE.1: 16 residues within 4Å: Chain A: R.156, T.176, G.178, H.179, R.180, P.246, N.324, Y.327, V.348, S.350, V.364, M.366, P.367, M.368, R.369 Ligands: 1PE.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.176, A:P.246, A:V.364, A:M.366 Hydrogen bonds: A:R.156, A:R.156, A:G.178, A:M.366, A:P.367, A:R.369 Water bridges: A:N.324, A:Y.327 Salt bridges: A:R.156 ACE-GLN-ALC-LV8-LEU-PHE.9: 16 residues within 4Å: Chain B: R.156, T.176, G.178, H.179, R.180, P.246, N.324, Y.327, V.348, S.350, V.364, M.366, P.367, M.368, R.369 Ligands: 1PE.15 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.176, B:P.246, B:V.364, B:M.366 Hydrogen bonds: B:R.156, B:R.156, B:G.178, B:M.366, B:P.367, B:R.369 Water bridges: B:N.324 Salt bridges: B:R.156

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: R.172, V.183, S.185, Y.248, Q.359, S.360, A.362 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.172, A:S.185, A:S.185, A:S.185, A:Y.248 Water bridges: A:Q.359, A:A.361 GOL.3: 2 residues within 4Å: Chain A: V.155, Y.157 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.155 GOL.4: 3 residues within 4Å: Chain A: L.266, L.310, D.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.311, A:D.311 Water bridges: A:D.311 GOL.5: 5 residues within 4Å: Chain A: R.283, S.326, L.329, D.330, N.333 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.283, A:D.330, A:D.330, A:N.333 GOL.10: 7 residues within 4Å: Chain B: R.172, V.183, S.185, Y.248, Q.359, S.360, A.362 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.172, B:S.185, B:S.185, B:S.185, B:Y.248 Water bridges: B:Q.359, B:A.361 GOL.11: 2 residues within 4Å: Chain B: V.155, Y.157 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.155 GOL.12: 3 residues within 4Å: Chain B: L.266, L.310, D.311 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.311, B:D.311 Water bridges: B:D.311 GOL.13: 5 residues within 4Å: Chain B: R.283, S.326, L.329, D.330, N.333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.283, B:D.330, B:N.333

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 7 residues within 4Å: Chain A: Q.19, S.22, L.25, G.26, R.77, F.80, R.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.22, A:R.77, A:R.77, A:R.84 1PE.7: 4 residues within 4Å: Chain A: R.369 Ligands: ACE-GLN-ALC-LV8-LEU-PHE.1, ACE-GLN-ALC-LV8-LEU-PHE.1, ACE-GLN-ALC-LV8-LEU-PHE.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.369, A:R.369 1PE.8: 6 residues within 4Å: Chain A: N.216, P.217, R.219, H.230, V.231, G.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.232 1PE.14: 7 residues within 4Å: Chain B: Q.19, S.22, L.25, G.26, R.77, F.80, R.84 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.22, B:R.77, B:R.77, B:R.84 1PE.15: 4 residues within 4Å: Chain B: R.369 Ligands: ACE-GLN-ALC-LV8-LEU-PHE.9, ACE-GLN-ALC-LV8-LEU-PHE.9, ACE-GLN-ALC-LV8-LEU-PHE.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.369, B:R.369 1PE.16: 6 residues within 4Å: Chain B: N.216, P.217, R.219, H.230, V.231, G.232 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Compain, G. et al., Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp. Jacs Au (2024)

Release Date

2024-03-13

Peptides

Beta sliding clamp: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta sliding clamp