SMTL ID : 4ovh.1

E. coli sliding clamp in complex with (R)-6-bromo-9-(2-(carboxymethylamino)-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: D.342, V.344, S.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.344 PEG.2: 3 residues within 4Å: Chain A: D.121, W.122, R.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.224, A:R.224 PEG.3: 6 residues within 4Å: Chain A: E.161, E.163, R.168, D.243, Y.244, R.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.243 Water bridges: A:Y.244, A:R.245 PEG.4: 5 residues within 4Å: Chain A: H.9, R.56, V.57, A.58, D.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56, A:R.56, A:A.58 PEG.8: 5 residues within 4Å: Chain A: Q.265 Chain B: R.7, R.80, L.82, E.84 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.7, B:R.7, B:E.84 Water bridges: A:Q.265

1 x 2VE: (2R)-6-bromo-9-{2-[(carboxymethyl)amino]-2-oxoethyl}-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid(Non-covalent)

2VE.5: 11 residues within 4Å: Chain A: R.152, Y.154, T.172, G.174, H.175, R.176, L.177, P.242, V.247, V.360, M.362 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.242 Hydrogen bonds: A:Y.154, A:G.174 Salt bridges: A:R.152, A:R.152, A:H.175 Halogen bonds: A:V.360

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

CL.6: 2 residues within 4Å: Chain A: S.181, S.356 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 1 residues within 4Å: Chain A: E.334 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.334

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.9: 4 residues within 4Å: Chain B: D.121, W.122, Q.217, R.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.217, B:R.224, B:R.224

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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