SMTL ID : 7az7.1

DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x SJ2- GLN- ALC- SOQ- LEU- ZCL: Peptide 37(Non-covalent)

SJ2-GLN-ALC-SOQ-LEU-ZCL.1: 18 residues within 4Å: Chain A: R.172, L.175, T.192, G.194, H.195, R.196, L.197, P.262, V.267, F.298, N.340, Y.343, V.380, M.382, P.383, M.384, R.385, L.386 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.197, A:V.380, A:M.382, A:R.385 Hydrogen bonds: A:G.194, A:M.382, A:P.383, A:R.385, A:L.386 Water bridges: A:R.172, A:R.172 Salt bridges: A:H.195 Halogen bonds: A:T.192 SJ2-GLN-ALC-SOQ-LEU-ZCL.4: 18 residues within 4Å: Chain B: R.172, L.175, T.192, G.194, H.195, R.196, L.197, P.262, V.267, F.298, N.340, Y.343, V.380, M.382, P.383, M.384, R.385, L.386 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.197, B:V.380, B:M.382, B:R.385 Hydrogen bonds: B:G.194, B:M.382, B:P.383, B:R.385, B:L.386 Water bridges: B:R.172, B:R.172, B:Y.343 Salt bridges: B:H.195 Halogen bonds: B:T.192

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: V.199, S.201, Y.264, Q.375, S.376, A.378 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.376 FMT.5: 6 residues within 4Å: Chain B: V.199, S.201, Y.264, Q.375, S.376, A.378 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.376

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

1PE.3: 8 residues within 4Å: Chain A: Q.35, S.38, L.41, G.42, A.92, R.93, F.96, R.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.38, A:R.93, A:R.93, A:R.100 1PE.6: 8 residues within 4Å: Chain B: Q.35, S.38, L.41, G.42, A.92, R.93, F.96, R.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.38, B:R.93, B:R.93, B:R.100

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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