SMTL ID : 7az5.1 (1 other biounit)

DNA polymerase sliding clamp from Escherichia coli with peptide 47 bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

2 x ACE- GLN- ALC- ASP- LEU- OIC- LEU: Peptide 47(Non-covalent)

ACE-GLN-ALC-ASP-LEU-OIC-LEU.1: 15 residues within 4Å: Chain A: T.192, G.194, H.195, R.196, L.197, P.262, R.266, 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: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 Water bridges: A:R.172 Salt bridges: A:R.266 ACE-GLN-ALC-ASP-LEU-OIC-LEU.2: 17 residues within 4Å: Chain B: T.192, G.194, H.195, R.196, L.197, P.262, R.266, V.267, N.340, Y.343, V.364, V.380, M.382, P.383, M.384, R.385, L.386 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.197, B:P.262, B:P.262, B:V.267, B:V.267, B:V.364, B:V.380, B:M.382, B:P.383, B:R.385 Hydrogen bonds: B:G.194, B:H.195, B:M.382, B:P.383, B:R.385 Water bridges: B:R.172, B:Y.343 Salt bridges: B:R.266

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 7 residues within 4Å: Chain A: Q.35, S.38, L.41, G.42, G.43, R.93, F.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.35, A:S.38 PG4.5: 5 residues within 4Å: Chain B: Q.35, S.38, L.41, R.93, F.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.38, B:R.93, B:R.93

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

PEG.4: 5 residues within 4Å: Chain A: L.54, Q.56, A.87, A.133, A.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.56 Water bridges: A:N.138 PEG.6: 6 residues within 4Å: Chain B: R.27, R.100, G.101, L.102, P.103, E.104 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:Q.285, B:G.101 Hydrogen bonds: B:R.27, B:R.27, 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
B

Beta sliding clamp

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