SMTL ID : 7az6.1

DNA polymerase sliding clamp from Escherichia coli with peptide 36 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x ACE- ARG- GLN- ALC- SOQ- LEU- ZCL: Peptide 36(Non-covalent)

ACE-ARG-GLN-ALC-SOQ-LEU-ZCL.1: 17 residues within 4Å: Chain A: R.172, L.175, 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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:H.195, A:L.197, A:V.364, A:V.380, A:M.382, A:P.383, A:R.385 Hydrogen bonds: A:G.194, A:M.382, A:P.383, A:R.385, A:R.385 Water bridges: A:R.172, A:G.194, A:Y.343 Salt bridges: A:H.195 Halogen bonds: A:T.192 ACE-ARG-GLN-ALC-SOQ-LEU-ZCL.7: 17 residues within 4Å: Chain B: R.172, L.175, 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 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:H.195, B:L.197, B:V.364, B:V.380, B:M.382, B:P.383, B:R.385 Hydrogen bonds: B:G.194, B:M.382, B:P.383, B:R.385, B:R.385, B:R.385 Water bridges: B:R.172, B:G.194 Salt bridges: B:H.195 Halogen bonds: B:T.192

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

PEG.2: 4 residues within 4Å: Chain A: S.38, R.93, F.96 Ligands: PEG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.38 Water bridges: A:R.93 PEG.3: 4 residues within 4Å: Chain A: Q.35, G.39, R.225 Ligands: PEG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.35 PEG.8: 4 residues within 4Å: Chain B: S.38, R.93, F.96 Ligands: PEG.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.38 Water bridges: B:R.93 PEG.9: 4 residues within 4Å: Chain B: Q.35, G.39, R.225 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.35

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: L.351, K.352, D.371 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.352, A:D.371 Water bridges: A:R.157, A:K.352 GOL.10: 3 residues within 4Å: Chain B: L.351, K.352, D.371 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.352 Water bridges: B:R.157, B:K.352

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain A: V.199, S.201, Q.375, S.376, A.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.201, A:Q.375 ACT.11: 5 residues within 4Å: Chain B: V.199, S.201, Q.375, S.376, A.377 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.201, B:Q.375

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain A: V.25, E.26, H.29, Q.81 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: V.25, E.26, H.29, Q.81 Ligand excluded by PLIP

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
A

Beta sliding clamp

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