SMTL ID : 7azd.1 (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: 15 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, 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:P.262, A:V.267, A:V.364, A:M.382, A:R.385 Hydrogen bonds: A:G.194, A:M.382, A:P.383, A:R.385 Salt bridges: A:R.172 SGZ-GLN-ALC-ASP-LEU-PHE.2: 16 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 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:M.382, B:P.383 Hydrogen bonds: B:G.194, B:M.382, B:P.383, B:R.385 Water bridges: B:N.340 Salt bridges: B:H.195

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

1PE.3: 6 residues within 4Å: Chain A: Q.35, S.38, L.41, G.42, R.93, F.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.35, A:S.38

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

PEG.4: 4 residues within 4Å: Chain A: R.76, V.77, A.78, D.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.78

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
A

B
D

Beta sliding clamp

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