SMTL ID : 6fvl.1 (1 other biounit)

DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-dimer

Ligands

2 x ACE- GLN- ALC- ASP- LEU- PHE: P7 peptide(Non-covalent)

ACE-GLN-ALC-ASP-LEU-PHE.1: 16 residues within 4Å: Chain A: T.174, G.176, H.177, R.178, L.179, P.244, V.249, Y.325, V.346, V.362, M.364, P.365, M.366, R.367 Ligands: GOL.6, GOL.17 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.174, A:L.179, A:P.244, A:V.249, A:V.362, A:R.367 Hydrogen bonds: A:G.176, A:G.176, A:M.364, A:P.365, A:R.367 Salt bridges: A:H.177 ACE-GLN-ALC-ASP-LEU-PHE.2: 19 residues within 4Å: Chain B: L.157, T.174, G.176, H.177, R.178, L.179, P.244, V.249, N.322, Y.325, V.346, S.348, V.362, M.364, P.365, M.366, R.367 Ligands: 1PE.18, GOL.19 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.157, B:T.174, B:L.179, B:P.244, B:V.346, B:V.362, B:R.367 Hydrogen bonds: B:G.176, B:M.364, B:P.365, B:R.367 Water bridges: B:N.322

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

1PE.3: 5 residues within 4Å: Chain A: Q.17, S.20, G.24, R.75, F.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.17, A:S.20, A:R.75, A:R.75 1PE.4: 6 residues within 4Å: Chain A: A.273, I.274, S.276, E.278, R.281 Chain B: D.79 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.79, A:S.276 1PE.5: 6 residues within 4Å: Chain A: H.11, R.58, V.59, A.60, V.62, D.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.60 1PE.8: 4 residues within 4Å: Chain B: S.20, L.23, R.75, F.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.20, B:R.75 Water bridges: B:R.75 1PE.9: 6 residues within 4Å: Chain B: R.139, E.142, N.331, A.332, K.334 Ligands: 1PE.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.142, B:K.334 1PE.10: 2 residues within 4Å: Chain B: Q.151, D.152 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.158 1PE.11: 7 residues within 4Å: Chain B: E.163, T.164, E.165, S.192, H.193, S.194, R.247 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.194 1PE.12: 4 residues within 4Å: Chain B: P.215, R.217, H.228, G.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.230 1PE.13: 2 residues within 4Å: Chain B: R.139 Ligands: 1PE.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.139 1PE.14: 7 residues within 4Å: Chain B: H.11, T.43, R.58, V.59, A.60, V.62, D.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.43, B:A.60 1PE.18: 6 residues within 4Å: Chain B: V.346, M.364, R.367 Ligands: ACE-GLN-ALC-ASP-LEU-PHE.2, ACE-GLN-ALC-ASP-LEU-PHE.2, ACE-GLN-ALC-ASP-LEU-PHE.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.367, B:R.367

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: R.367 Ligands: ACE-GLN-ALC-ASP-LEU-PHE.1 No protein-ligand interaction detected (PLIP) GOL.7: 1 residues within 4Å: Chain A: N.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.297 Water bridges: A:N.297 GOL.15: 9 residues within 4Å: Chain B: S.1, A.69, T.70, L.94, G.96, E.97, T.112, P.114, A.115 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.96, B:T.112, B:T.112, B:A.115 GOL.16: 3 residues within 4Å: Chain B: R.284, N.297, L.368 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.284, B:N.297 Water bridges: B:N.297, B:N.297, B:L.368 GOL.17: 2 residues within 4Å: Chain A: H.177 Ligands: ACE-GLN-ALC-ASP-LEU-PHE.1 No protein-ligand interaction detected (PLIP) GOL.19: 3 residues within 4Å: Chain B: R.154 Ligands: ACE-GLN-ALC-ASP-LEU-PHE.2, ACE-GLN-ALC-ASP-LEU-PHE.2 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andre, C. et al., Peptide Interactions on Bacterial Sliding Clamps. Acs Infect Dis. (2019)

Release Date

2019-04-10

Peptides

Beta sliding clamp: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta sliding clamp

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