SMTL ID : 7az5.2 (1 other biounit)

DNA polymerase sliding clamp from Escherichia coli with peptide 47 bound

Coordinates

PDB Format Compare

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: 16 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, V.380, M.382, P.383, M.384, R.385 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.197, A:P.262, A:P.262, A:V.267, A:V.267, A:V.364, A:V.380, A:M.382 Hydrogen bonds: A:G.194, A:G.194, A:M.382, A:P.383, A:R.385 Water bridges: A:N.340, A:Y.343 Salt bridges: A:R.266 ACE-GLN-ALC-ASP-LEU-OIC-LEU.2: 14 residues within 4Å: Chain B: T.192, G.194, H.195, R.196, P.262, R.266, V.267, N.340, Y.343, V.364, M.382, P.383, M.384, R.385 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.262, B:P.262, B:V.267, B:V.267, B:V.364, B:M.382 Hydrogen bonds: B:G.194, B:M.382, B:P.383, B:R.385 Salt bridges: B:R.266

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

PEG.3: 5 residues within 4Å: Chain A: R.27, R.100, L.102, P.103, E.104 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.27, A:R.27, A:R.100 Water bridges: A:R.100, A:E.104

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

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

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
C

B
D

Beta sliding clamp

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