SMTL ID : 4ovg.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x 2VF: (2R)-9-(2-amino-2-oxoethyl)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid(Non-covalent)

2VF.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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.172, A:P.242 Hydrogen bonds: A:Y.154, A:G.174 Salt bridges: A:R.152 Halogen bonds: A:V.360 2VF.11: 11 residues within 4Å: Chain B: R.152, Y.154, L.155, T.172, G.174, H.175, R.176, L.177, P.242, V.247, M.362 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.155, B:P.242 Salt bridges: B:R.152

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

PEG.2: 4 residues within 4Å: Chain A: R.56, V.57, A.58, D.229 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.58 PEG.3: 4 residues within 4Å: Chain A: E.257, D.307, V.308, T.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.309 PEG.12: 5 residues within 4Å: Chain B: Q.15, Q.16, G.19, E.202, R.205 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.202, B:R.205 Water bridges: B:Q.16, B:G.19, B:E.202 PEG.13: 4 residues within 4Å: Chain B: T.129, P.213, R.215, H.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.129, B:T.129, B:R.215, B:H.226

4 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: E.334 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.334, A:E.334, H2O.8, H2O.10 CA.6: 1 residues within 4Å: Chain A: S.345 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: T.110, L.111 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.6, H2O.6, H2O.9, H2O.9, H2O.10 CA.8: 2 residues within 4Å: Chain A: S.181, S.356 No protein-ligand interaction detected (PLIP)

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

PG4.5: 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 PG4.14: 3 residues within 4Å: Chain B: D.121, W.122, R.224 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.122, B:Q.217, B:R.224, B:R.224 Water bridges: B:S.124

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 3 residues within 4Å: Chain A: D.261, K.264, Q.265 No protein-ligand interaction detected (PLIP)

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

CL.10: 3 residues within 4Å: Chain A: Q.265, R.269 Chain B: P.83 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: N.275, K.277, F.278 Ligand excluded by PLIP

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

PGE.15: 5 residues within 4Å: Chain B: S.18, L.21, G.23, R.73, F.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.73

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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