SMTL ID : 6fvm.1

Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

2 x ACE- GLN- ALC- ASP- LEU- PHE: P7 peptide(Non-covalent)

ACE-GLN-ALC-ASP-LEU-PHE.1: 16 residues within 4Å: Chain A: R.154, T.174, G.176, H.177, R.178, L.179, P.244, V.249, N.322, Y.325, V.346, V.362, M.364, P.365, M.366, R.367 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:T.174, A:L.179, A:P.244, A:V.362, A:R.367 Hydrogen bonds: A:R.154, A:G.176, A:G.176, A:M.364, A:P.365, A:R.367 Water bridges: A:N.322, A:Y.325 ACE-GLN-ALC-ASP-LEU-PHE.2: 16 residues within 4Å: Chain B: R.154, T.174, G.176, H.177, R.178, L.179, P.244, V.249, N.322, Y.325, V.346, V.362, M.364, P.365, M.366, R.367 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.174, B:L.179, B:P.244, B:V.249, B:V.346, B:V.362, B:R.367 Hydrogen bonds: B:G.176, B:H.177, B:M.364, B:P.365, B:R.367 Water bridges: B:R.154

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: V.7, E.8, H.11, Q.63 No protein-ligand interaction detected (PLIP)

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

1PE.4: 5 residues within 4Å: Chain A: R.9, R.82, G.83, L.84, E.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.9, A:R.9 1PE.5: 6 residues within 4Å: Chain A: H.11, R.58, V.59, A.60, V.62, D.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.60 Water bridges: A:V.62 1PE.6: 5 residues within 4Å: Chain A: S.20, L.23, G.24, R.75, F.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.20, A:R.75, A:R.75 1PE.7: 3 residues within 4Å: Chain A: Y.286, K.293, E.305 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.293, A:E.305 1PE.9: 7 residues within 4Å: Chain B: S.20, L.23, G.24, G.25, R.75, F.78, R.82 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.20, B:R.75, B:R.75, B:R.82 1PE.10: 6 residues within 4Å: Chain B: E.163, E.165, S.192, H.193, S.194, R.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.165 Water bridges: B:S.194 1PE.11: 6 residues within 4Å: Chain B: H.11, R.58, V.59, A.60, V.62, D.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.60 1PE.12: 3 residues within 4Å: Chain A: L.264 Chain B: P.85, E.86 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.86 1PE.13: 9 residues within 4Å: Chain B: L.161, S.194, I.196, G.241, R.242, F.243, P.244, D.245, Y.246 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.246 Hydrogen bonds: B:I.196, B:F.243 Water bridges: B:S.194

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: S.194, V.195, I.196, G.241, R.242, F.243 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:F.243, A:F.243 Water bridges: A:I.196, A:V.239, A:V.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andre, C. et al., Peptide Interactions on Bacterial Sliding Clamps. Acs Infect Dis. (2019)

Release Date

2019-04-10

Peptides

Beta sliding clamp: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Beta sliding clamp