SMTL ID : 3d1f.1

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SER- GLU- GLN- VAL- GLU- LEU- GLU- PHE- ASP: Nonapeptide from polymerase III C-terminal(Non-covalent)

SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.1: 18 residues within 4Å: Chain A: T.172, G.174, H.175, R.176, L.177, P.242, D.243, R.246, V.247, F.278, Y.323, V.344, V.360, M.362, P.363, M.364, R.365 Ligands: 323.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.177, A:P.242, A:V.247, A:V.360, A:R.365 Hydrogen bonds: A:G.174, A:G.174, A:R.246, A:M.362, A:P.363, A:R.365 Water bridges: A:R.152, A:R.365 Salt bridges: A:H.175 SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.2: 18 residues within 4Å: Chain B: T.172, G.174, H.175, R.176, P.242, R.246, V.247, F.278, N.320, Y.323, V.344, V.360, M.362, P.363, M.364, R.365, L.366 Ligands: 323.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.242, B:P.242, B:V.247, B:V.247, B:V.360, B:L.366 Hydrogen bonds: B:G.174, B:M.362, B:P.363, B:R.365 Water bridges: B:R.152, B:R.152, B:Y.323 Salt bridges: B:H.175, B:R.246, B:K.250

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

PEG.3: 2 residues within 4Å: Chain A: E.6, H.9 No protein-ligand interaction detected (PLIP) PEG.4: 3 residues within 4Å: Chain A: E.8, K.12, P.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.8

2 x 323: 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate(Non-covalent)

323.5: 3 residues within 4Å: Chain A: R.365 Ligands: SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.1, SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.1 No protein-ligand interaction detected (PLIP) 323.6: 3 residues within 4Å: Chain B: R.365 Ligands: SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.2, SER-GLU-GLN-VAL-GLU-LEU-GLU-PHE-ASP.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Georgescu, R.E. et al., Structure of a small-molecule inhibitor of a DNA polymerase sliding clamp. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-07-29

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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