SMTL ID : 7az8.1

DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

homo-dimer

Ligands

2 x TCA- GLN- ALC- ASP- LEU- PRO- LEU: Peptide 43(Non-covalent)

TCA-GLN-ALC-ASP-LEU-PRO-LEU.1: 17 residues within 4Å: Chain A: L.175, T.192, G.194, H.195, R.196, L.197, P.262, V.267, F.298, N.340, Y.343, V.364, V.380, M.382, P.383, M.384, R.385 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.175, A:T.192, 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 pi-Stacking: A:F.298 TCA-GLN-ALC-ASP-LEU-PRO-LEU.2: 15 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, V.380, M.382, P.383, M.384, R.385 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.197, B:V.267, B:V.364, B:V.380, B:M.382, B:R.385 Hydrogen bonds: B:G.194, B:G.194, B:M.382, B:P.383, B:R.385 Water bridges: B:Y.343

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

PEG.3: 5 residues within 4Å: Chain A: Q.56, V.57, A.58, G.86, A.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.57, A:G.86 Water bridges: A:G.18 PEG.4: 6 residues within 4Å: Chain A: H.29, R.76, V.77, A.78, V.80, D.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.29, A:A.78, A:D.249 PEG.5: 2 residues within 4Å: Chain A: Y.173 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.6: 3 residues within 4Å: Chain A: Y.173, D.258 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.176, A:D.258 PEG.10: 4 residues within 4Å: Chain B: E.185, P.203, I.204, G.205 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.185, B:I.204, B:G.205 PEG.11: 6 residues within 4Å: Chain B: L.34, Q.35, S.38, R.93, F.96, R.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.38, B:S.38, B:R.93, B:R.93, B:R.100

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

1PE.7: 8 residues within 4Å: Chain A: L.139, D.140, D.141, W.142, Q.143, S.144, Q.237, R.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.139, A:W.142, A:S.144, A:Q.237 1PE.8: 9 residues within 4Å: Chain A: L.34, 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: R.188, V.199, C.200, S.201, Y.264, Q.375, S.376, A.377, A.378 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.188, A:S.201, A:S.376 Water bridges: A:S.201, A:S.201, A:Q.375 GOL.12: 7 residues within 4Å: Chain B: R.188, V.199, S.201, Y.264, Q.375, S.376, A.378 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.188, B:S.201, B:Y.264, B:S.376 Water bridges: B:R.188, B:S.201, B:Q.375 GOL.13: 4 residues within 4Å: Chain B: W.142, S.144, Q.237, R.244 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.142, B:S.144, B:Q.237, B:Q.237 Water bridges: B:R.244 GOL.14: 8 residues within 4Å: Chain B: L.179, E.181, S.212, R.260, F.261, P.262, D.263, R.265 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.212, B:R.260 Water bridges: B:F.261, B:R.265, B:R.265 GOL.15: 6 residues within 4Å: Chain B: N.232, P.233, R.235, H.246, V.247, G.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.248, B:G.248

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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