SMTL ID : 4mjp.1

E. coli sliding clamp in complex with (R)-Vedaprofen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: D.121, W.122, R.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.217, A:R.224, A:R.224 PEG.5: 6 residues within 4Å: Chain A: Q.265 Chain B: R.7, R.80, G.81, L.82, E.84 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.7, B:R.7 Water bridges: A:R.269

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: R.7, L.11, R.80, L.82, E.84 Chain B: Q.265 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.7, A:R.7, B:Q.265 Water bridges: A:E.84 PGE.8: 4 residues within 4Å: Chain B: D.121, W.122, Q.217, R.224 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.121, B:R.224 Water bridges: B:S.124, B:Q.217

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: S.181, Q.355, S.356 No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain B: R.105 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: L.262, A.266, R.269 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x 27O: (2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid(Non-covalent)

27O.7: 10 residues within 4Å: Chain B: R.152, T.172, G.174, H.175, L.177, R.240, P.242, D.243, R.246, V.247 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.177, B:P.242, B:V.247, B:V.247 Hydrogen bonds: B:D.243 Water bridges: B:R.240 Salt bridges: B:R.240

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., DNA replication is the target for the antibacterial effects of nonsteroidal anti-inflammatory drugs. Chem.Biol. (2014)

Release Date

2013-09-18

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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