SMTL ID : 7azd.2 (1 other biounit)

DNA polymerase sliding clamp from Escherichia coli with peptide 20 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-dimer

Ligands

2 x SGZ- GLN- ALC- ASP- LEU- PHE: Peptide 20(Non-covalent)

SGZ-GLN-ALC-ASP-LEU-PHE.1: 16 residues within 4Å: Chain A: R.172, T.192, G.194, H.195, R.196, L.197, P.262, V.267, N.340, Y.343, V.364, V.380, M.382, P.383, M.384, R.385 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.192, A:L.197, A:P.262, A:V.267, A:V.364, A:V.380, A:R.385 Hydrogen bonds: A:R.172, A:G.194, A:M.382, A:P.383, A:R.385 Salt bridges: A:H.195 SGZ-GLN-ALC-ASP-LEU-PHE.2: 19 residues within 4Å: Chain B: R.172, T.192, G.194, H.195, R.196, L.197, P.262, D.263, R.266, V.267, N.340, Y.343, V.364, S.366, V.380, M.382, P.383, M.384, R.385 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.192, B:L.197, B:P.262, B:P.262, B:V.267, B:V.364, B:V.380, B:R.385 Hydrogen bonds: B:G.194, B:H.195, B:R.266, B:R.266, B:M.382, B:P.383, B:R.385 Salt bridges: B:R.172

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: Q.35, S.38, R.93, F.96 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.35, A:S.38, A:R.93 Water bridges: A:G.42 PEG.5: 5 residues within 4Å: Chain B: S.38, L.41, G.42, R.93, F.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.38, B:G.42, B:R.93

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

1PE.4: 9 residues within 4Å: Chain A: R.27, D.97, R.100, G.101, L.102, E.104 Chain B: Q.285, A.288, I.292 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.97, A:E.104 Water bridges: A:R.100, A:E.104, A:E.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Monsarrat, C. et al., Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp. J.Med.Chem. (2021)

Release Date

2021-12-01

Peptides

Beta sliding clamp: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Beta sliding clamp

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