SMTL ID : 4pnv.1

E. coli sliding clamp apo-crystal in P21 space group with larger cell dimensions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: N.118, L.119 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:L.119, H2O.2, H2O.2, H2O.4, H2O.6 CA.3: 4 residues within 4Å: Chain A: R.103, R.105 Chain B: E.303, I.305 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:R.103, B:E.303 CA.5: 4 residues within 4Å: Chain A: Y.153, N.156, G.157, V.237 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.153, H2O.1, H2O.10 CA.6: 4 residues within 4Å: Chain A: H.255, Y.310, S.311, G.312 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.255, H2O.15, H2O.16 CA.7: 3 residues within 4Å: Chain A: L.14, S.18, L.33 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.14, H2O.9 CA.8: 2 residues within 4Å: Chain B: N.118, L.119 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:L.119, H2O.18, H2O.20, H2O.21, H2O.24 CA.11: 5 residues within 4Å: Chain B: T.4, V.5, L.59, V.60, Q.61 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.4, H2O.18, H2O.23 CA.12: 3 residues within 4Å: Chain B: T.110, L.111, P.112 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.110, H2O.18, H2O.33

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

CL.2: 4 residues within 4Å: Chain A: V.5, E.6, H.9, Q.61 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: P.83 Chain B: Q.265, R.269 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: S.286, E.287, Q.289 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: Q.16, R.205, M.206, F.230 Ligand excluded by PLIP

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

PEG.4: 11 residues within 4Å: Chain A: V.17, S.18, G.19, L.30, G.31, N.32, L.33, G.46, T.47, M.53, A.72 No protein-ligand interaction detected (PLIP) PEG.9: 6 residues within 4Å: Chain B: M.1, P.65, G.66, A.67, L.92, A.113 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.1, B:A.67 Water bridges: B:M.1, B:M.1, B:A.114 PEG.10: 5 residues within 4Å: Chain B: Q.36, A.38, T.41, L.42, S.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.38, B:A.38, B:S.43, B:S.43

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. J.Med.Chem. (2015)

Release Date

2014-03-05

Peptides

DNA polymerase III subunit beta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA polymerase III subunit beta

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