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

DNA polymerase sliding clamp from Escherichia coli with peptide 35 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x ACE- GLN- ALC- SOQ- LEU- ZCL: Peptide 35(Non-covalent)

ACE-GLN-ALC-SOQ-LEU-ZCL.1: 17 residues within 4Å: Chain A: R.172, L.175, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.197, A:V.380, A:R.385 Hydrogen bonds: A:G.194, A:H.195, A:M.382, A:P.383, A:R.385 Water bridges: A:R.172, A:R.172, A:N.340 Salt bridges: A:H.195 Halogen bonds: A:T.192 ACE-GLN-ALC-SOQ-LEU-ZCL.2: 14 residues within 4Å: Chain B: R.172, T.192, G.194, H.195, R.196, P.262, Y.264, V.267, N.340, Y.343, M.382, P.383, M.384, R.385 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:P.262, B:V.267, B:M.382, B:R.385 Hydrogen bonds: B:G.194, B:M.382, B:P.383, B:R.385 Water bridges: B:Y.343 Salt bridges: B:R.172, B:H.195 Halogen bonds: B:T.192

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: L.69, K.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.255, A:K.255 GOL.8: 1 residues within 4Å: Chain B: E.323 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.323 Water bridges: B:A.322

1 x K: POTASSIUM ION(Non-covalent)

K.4: 3 residues within 4Å: Chain A: R.44, P.45, T.46 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.46

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

1PE.5: 5 residues within 4Å: Chain A: Y.304, Q.309, K.311, E.323, I.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.311, A:E.323, A:E.323 Water bridges: A:Q.309 1PE.6: 5 residues within 4Å: Chain A: R.27, R.100, L.102, E.104 Chain B: Q.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.27, A:R.27 1PE.9: 5 residues within 4Å: Chain B: S.38, L.41, R.93, F.96, R.100 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.38, B:R.93, B:R.93, B:R.100 1PE.10: 7 residues within 4Å: Chain A: Q.285, A.288, I.292 Chain B: D.97, R.100, G.101 Ligands: 1PE.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.100, B:R.100, A:Q.285 1PE.11: 8 residues within 4Å: Chain A: Q.285 Chain B: R.27, E.28, L.31, R.100, L.102, E.104 Ligands: 1PE.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.27, B:R.27

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 4 residues within 4Å: Chain A: E.26, H.29, V.80, Q.81 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: V.25, E.26, H.29, Q.81 Ligand excluded by PLIP

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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