SMTL ID : 4pnw.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

2VM.1: 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.242 Hydrogen bonds: A:Y.154 Salt bridges: A:R.152 Halogen bonds: A:V.360 2VM.5: 11 residues within 4Å: Chain B: Y.153, Y.154, T.172, D.173, G.174, H.175, R.176, L.177, P.242, V.360, M.362 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.242 Hydrogen bonds: B:G.174, B:G.174 Water bridges: B:H.175 Salt bridges: B:H.175 Halogen bonds: B:V.360

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 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.1, H2O.3, H2O.3, H2O.4 CA.3: 3 residues within 4Å: Chain A: S.181, Q.355, S.356 No protein-ligand interaction detected (PLIP) CA.6: 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.13, H2O.15, H2O.17, H2O.17 CA.7: 3 residues within 4Å: Chain B: S.181, Q.355, S.356 No protein-ligand interaction detected (PLIP)

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

CL.4: 4 residues within 4Å: Chain B: L.262, Q.265, A.266, R.269 Ligand excluded by PLIP

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

PEG.8: 5 residues within 4Å: Chain B: R.7, L.11, R.80, L.82, E.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.7, B:R.7, B:G.81 PEG.9: 3 residues within 4Å: Chain B: S.286, Q.289, K.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.286, B:K.291 PEG.10: 8 residues within 4Å: Chain B: K.2, F.3, A.89, V.90, Q.91, E.93, L.98, R.100 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.2, B:K.2, B:Q.91, B:R.100 Water bridges: B:Q.91, B:R.100

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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