SMTL ID : 4n96.1

E. coli sliding clamp in complex with 6-nitroindazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

1 x 6NI: 6-NITROINDAZOLE(Non-covalent)

6NI.1: 7 residues within 4Å: Chain A: T.172, G.174, P.242, V.247, S.346, V.360, M.362 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: G.46, T.47, E.202 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain A: E.6, E.8, G.85 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.6, H2O.4 CA.10: 3 residues within 4Å: Chain B: E.6, G.85, E.87 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.6, B:G.85, B:E.87, H2O.17

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

CL.3: 1 residues within 4Å: Chain A: A.58 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: H.226, I.231 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: S.181, S.356 Ligand excluded by PLIP

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

PEG.6: 6 residues within 4Å: Chain A: L.159, E.161, S.192, F.241, P.242, D.243 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.192, A:F.241 Water bridges: A:R.245 PEG.7: 4 residues within 4Å: Chain A: W.122, Q.123, S.124, R.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.122, A:Q.123, A:S.124 Water bridges: A:Q.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. J.Med.Chem. (2014)

Release Date

2013-11-06

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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