SMTL ID : 6fvl.2 (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: 14 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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.174, A:L.179, A:P.244, A:V.249, A:V.346, A:V.362, A:P.365, A:R.367 Hydrogen bonds: A:G.176, A:G.176, A:P.365, A:R.367 Water bridges: A:Y.325, A:Y.325, A:M.364, A:P.365 Salt bridges: A:H.177 ACE-GLN-ALC-ASP-LEU-PHE.2: 15 residues within 4Å: Chain B: 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: 1PE.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.174, B:L.179, B:P.244, B:V.249, B:V.346, B:V.362, B:R.367 Hydrogen bonds: B:G.176, B:M.364, B:P.365, B:R.367

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

1PE.3: 9 residues within 4Å: Chain A: E.259, A.260, G.261, D.309, V.310, T.311, E.336, N.337, A.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.259, A:N.337 1PE.4: 7 residues within 4Å: Chain A: P.85, A.88, S.103, G.104, R.105, S.106 Chain B: R.271 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.105 Water bridges: B:R.271 1PE.5: 4 residues within 4Å: Chain A: S.20, G.24, R.75, F.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.20, A:R.75 1PE.6: 4 residues within 4Å: Chain B: Y.156, R.242, P.244, D.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.156, B:D.245 1PE.7: 6 residues within 4Å: Chain A: Q.267 Chain B: R.9, R.82, G.83, L.84, E.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.9 1PE.9: 4 residues within 4Å: Chain B: V.346 Ligands: ACE-GLN-ALC-ASP-LEU-PHE.2, ACE-GLN-ALC-ASP-LEU-PHE.2, ACE-GLN-ALC-ASP-LEU-PHE.2 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain B: N.297, L.368 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.297 Water bridges: B:N.297, B:N.297

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
C

B
D

Beta sliding clamp

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