SMTL ID : 7aze.1

DNA polymerase sliding clamp from Escherichia coli with peptide 18 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

2 x SJ8- GLN- ALC- ASP- LEU- PHE: Peptide 18(Non-covalent)

SJ8-GLN-ALC-ASP-LEU-PHE.1: 18 residues within 4Å: Chain A: R.172, T.192, G.194, H.195, R.196, L.197, P.262, V.267, F.298, N.340, Y.343, V.364, S.366, V.380, M.382, P.383, M.384, R.385 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:T.192, A:L.197, A:P.262, A:V.267, A:V.364, A:V.380, 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, A:R.172 pi-Stacking: A:F.298 SJ8-GLN-ALC-ASP-LEU-PHE.2: 17 residues within 4Å: Chain B: T.192, G.194, H.195, R.196, L.197, P.262, V.267, N.340, Y.343, V.364, S.366, V.380, M.382, P.383, M.384, R.385 Ligands: 1PE.8 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:T.192, B:L.197, B:P.262, B:V.267, B:V.364, B:V.380, B:M.382, 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:G.194, B:Y.343 pi-Stacking: B:F.298

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 8 residues within 4Å: Chain A: R.188, V.199, S.201, Y.264, L.268, Q.375, S.376, A.378 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.199 Hydrogen bonds: A:S.201, A:Q.375 Water bridges: A:Q.368 Salt bridges: A:R.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.285 Chain B: R.27, R.100, G.101, L.102, P.103 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.285, B:R.27, B:G.101, B:E.104 Water bridges: B:R.27 GOL.6: 10 residues within 4Å: Chain B: R.188, V.199, C.200, S.201, Y.264, L.268, Q.375, S.376, A.377, A.378 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.201, B:S.201, B:A.377 Water bridges: B:R.188, B:Y.264, B:Y.264

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

1PE.5: 6 residues within 4Å: Chain A: Q.35, S.38, G.42, 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.7: 6 residues within 4Å: Chain B: Q.35, S.38, G.42, R.93, F.96, R.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.38, B:R.93, B:R.93, B:R.100 Water bridges: B:R.100 1PE.8: 7 residues within 4Å: Chain B: R.260, F.261, P.262, D.263, R.266, V.267 Ligands: SJ8-GLN-ALC-ASP-LEU-PHE.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.263, B:R.266

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

Related Entries With Identical Sequence