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

DNA polymerase sliding clamp from Escherichia coli with peptide 8 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x SGK- GLN- ALC- ASP- LEU- PHE: Peptide 8(Non-covalent)

SGK-GLN-ALC-ASP-LEU-PHE.1: 16 residues within 4Å: Chain A: T.175, G.177, H.178, R.179, L.180, P.245, V.250, N.323, Y.326, V.347, V.363, M.365, P.366, M.367, R.368, L.369 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.175, A:L.180, A:P.245, A:V.250, A:V.250, A:V.363, A:M.365 Hydrogen bonds: A:G.177, A:M.365, A:P.366, A:R.368, A:R.368 Water bridges: A:N.323 SGK-GLN-ALC-ASP-LEU-PHE.2: 17 residues within 4Å: Chain B: T.175, G.177, H.178, R.179, L.180, P.245, V.250, F.281, N.323, Y.326, V.347, S.349, V.363, M.365, P.366, M.367, R.368 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.175, B:L.180, B:P.245, B:V.250, B:F.281, B:V.347, B:V.363, B:M.365, B:R.368 Hydrogen bonds: B:G.177, B:H.178, B:M.365, B:P.366, B:R.368 Water bridges: B:R.155, B:R.155, B:R.155

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.182, S.184, Y.247, L.251, Q.358, S.359, A.361 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.247, A:Y.247, A:S.359

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

PEG.4: 4 residues within 4Å: Chain A: R.59, V.60, A.61, D.232 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.61 Water bridges: A:R.59, A:D.232

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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