SMTL ID : 4n99.1

E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x 2J1: 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid(Non-covalent)

2J1.1: 9 residues within 4Å: Chain A: R.152, T.172, G.174, H.175, R.176, P.242, V.247, S.346, M.362 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.242, A:P.242, A:V.247 Hydrogen bonds: A:S.346

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

PEG.2: 3 residues within 4Å: Chain A: S.286, E.287, Q.289 Ligand excluded by PLIP PEG.3: 3 residues within 4Å: Chain A: W.122, Q.217, R.224 Ligand excluded by PLIP PEG.5: 4 residues within 4Å: Chain A: Q.36, S.43, R.56, I.231 Ligand excluded by PLIP PEG.6: 4 residues within 4Å: Chain A: R.80, G.81, P.83 Chain B: Q.265 Ligand excluded by PLIP PEG.8: 7 residues within 4Å: Chain A: S.181, L.248, Q.348, E.350, Q.355, S.356, A.358 Ligand excluded by PLIP PEG.12: 8 residues within 4Å: Chain A: L.262, A.266, R.269, I.305, L.306, D.307 Ligands: PG4.19, PEG.33 Ligand excluded by PLIP PEG.13: 1 residues within 4Å: Chain A: E.64 Ligand excluded by PLIP PEG.14: 5 residues within 4Å: Chain A: Q.299, E.301 Chain B: S.107 Ligands: PG4.30, CA.35 Ligand excluded by PLIP PEG.18: 1 residues within 4Å: Chain A: R.137 Ligand excluded by PLIP PEG.21: 7 residues within 4Å: Chain B: E.52, V.54, R.56, N.118, L.119, R.224, I.231 Ligand excluded by PLIP PEG.23: 6 residues within 4Å: Chain B: R.215, Q.217, R.224, H.226, I.231 Ligands: PEG.31 Ligand excluded by PLIP PEG.25: 4 residues within 4Å: Chain B: R.56, H.226, G.228, D.229 Ligand excluded by PLIP PEG.26: 7 residues within 4Å: Chain B: E.50, Y.153, N.156, G.157, P.196, R.197, V.237 Ligand excluded by PLIP PEG.27: 1 residues within 4Å: Ligands: PEG.32 Ligand excluded by PLIP PEG.28: 5 residues within 4Å: Chain A: E.276 Chain B: P.71, R.73, K.74 Ligands: PEG.34 Ligand excluded by PLIP PEG.31: 6 residues within 4Å: Chain B: D.121, W.122, S.124, Q.217, R.224 Ligands: PEG.23 Ligand excluded by PLIP PEG.32: 10 residues within 4Å: Chain B: V.179, C.180, S.181, Y.244, L.248, Q.348, E.350, Q.355, S.356 Ligands: PEG.27 Ligand excluded by PLIP PEG.33: 11 residues within 4Å: Chain A: R.269, I.305 Chain B: L.82, P.83, A.86, S.101, G.102, R.103, S.104 Ligands: PEG.12, PG4.19 Ligand excluded by PLIP PEG.34: 5 residues within 4Å: Chain B: G.23, P.25, R.73 Ligands: PG4.20, PEG.28 Ligand excluded by PLIP

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

PG4.4: 8 residues within 4Å: Chain A: A.268, A.271, I.272, R.279, L.325 Chain B: D.77, R.80, G.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.77, B:R.80 PG4.10: 7 residues within 4Å: Chain A: P.83, S.101, G.102, R.103, S.104 Chain B: L.262, R.269 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.103, A:R.103, A:R.103 Water bridges: B:R.269 PG4.15: 3 residues within 4Å: Chain A: P.112, A.114, D.115 No protein-ligand interaction detected (PLIP) PG4.16: 3 residues within 4Å: Chain A: R.105 Chain B: Q.289, I.305 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.105 Hydrogen bonds: B:Q.289, B:K.291 PG4.19: 7 residues within 4Å: Chain A: D.261, L.262, Q.265, R.269 Chain B: P.83 Ligands: PEG.12, PEG.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.269, A:R.269 PG4.20: 6 residues within 4Å: Chain B: S.18, L.21, R.73, F.76, R.80 Ligands: PEG.34 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.18, B:R.73, B:R.73, B:R.80 Water bridges: B:R.80 PG4.22: 5 residues within 4Å: Chain A: Q.265 Chain B: R.7, R.80, G.81, L.82 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.265, B:R.7, B:R.7 PG4.24: 8 residues within 4Å: Chain B: K.264, Q.265, A.268, A.271, I.272, R.279, L.325, N.329 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.265, B:R.279, B:R.279, B:N.329 PG4.29: 6 residues within 4Å: Chain B: A.67, L.92, G.94, P.112, A.113, A.114 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.94, B:A.113, B:A.114 PG4.30: 5 residues within 4Å: Chain A: E.301, E.303 Chain B: R.105, S.107 Ligands: PEG.14 No protein-ligand interaction detected (PLIP)

5 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain A: V.57, A.58 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain A: R.282, E.316, L.366 No protein-ligand interaction detected (PLIP) CA.11: 2 residues within 4Å: Chain A: G.228, D.229 No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain A: E.314 No protein-ligand interaction detected (PLIP) CA.35: 4 residues within 4Å: Chain B: E.93, L.98, S.107 Ligands: PEG.14 No protein-ligand interaction detected (PLIP)

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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