SMTL ID : 3kti.1

Structure of ClpP in complex with ADEP1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-heptamer

Ligands

7 x OTT- PHE- SER- PRO- MAA- ALA- MP8: Acyldepsipeptide 1(Non-covalent)

OTT-PHE-SER-PRO-MAA-ALA-MP8.1: 17 residues within 4Å: Chain A: V.44, L.48, F.49, A.52, T.79, F.82 Chain B: R.22, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.2: 16 residues within 4Å: Chain A: R.22, D.26, I.28, E.58, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Chain G: L.48, A.52, T.79, F.82 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.3: 15 residues within 4Å: Chain E: V.44, L.48, F.49, T.79, F.82 Chain F: D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.4: 18 residues within 4Å: Chain B: V.44, L.48, F.49, A.52, T.79, F.82 Chain C: R.22, D.26, I.28, E.58, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.5: 18 residues within 4Å: Chain C: V.44, L.48, F.49, A.52, T.79, F.82 Chain D: R.22, L.23, D.26, I.28, E.58, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.6: 17 residues within 4Å: Chain D: V.44, L.48, F.49, T.79, F.82 Chain E: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available OTT-PHE-SER-PRO-MAA-ALA-MP8.7: 17 residues within 4Å: Chain F: L.48, F.49, A.52, T.79, F.82 Chain G: R.22, L.23, D.26, I.28, E.58, S.60, Y.62, S.88, I.90, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available

7 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 6 residues within 4Å: Chain A: S.97, I.121, H.122, Q.123, P.124, L.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.122 DMS.10: 5 residues within 4Å: Chain B: S.97, I.121, H.122, N.150, L.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.122 DMS.12: 4 residues within 4Å: Chain C: S.97, I.121, H.122, L.153 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.122 DMS.14: 5 residues within 4Å: Chain D: S.97, I.121, H.122, L.149, L.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.122 DMS.16: 4 residues within 4Å: Chain E: S.97, I.121, H.122, L.153 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.122 DMS.18: 4 residues within 4Å: Chain F: S.97, I.121, H.122, L.153 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.122 DMS.20: 5 residues within 4Å: Chain G: S.97, I.121, H.122, P.124, L.153 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:H.122

7 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.9: 8 residues within 4Å: Chain A: S.69, I.70, T.71, R.141, L.145 Chain B: P.66, M.94, F.173 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.69, A:I.70, A:T.71 Salt bridges: A:R.141 Hydrophobic interactions: B:P.66, B:F.173 NHE.11: 7 residues within 4Å: Chain B: S.69, I.70, T.71, R.141, L.145 Chain C: P.66, M.94 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:S.69, B:I.70, B:T.71 Water bridges: B:S.69, B:L.125 Salt bridges: B:R.141 Hydrophobic interactions: C:P.66 NHE.13: 7 residues within 4Å: Chain C: S.69, I.70, T.71, R.141 Chain D: P.66, M.94, F.173 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.69, C:I.70, C:T.71 Water bridges: C:G.68, C:S.69 Salt bridges: C:R.141 Hydrophobic interactions: D:P.66, D:F.173 NHE.15: 8 residues within 4Å: Chain D: S.69, I.70, T.71, R.141, L.145 Chain E: P.66, M.94, F.173 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain D Hydrophobic interactions: E:P.66, E:F.173 Hydrogen bonds: D:S.69, D:I.70, D:T.71, D:R.141 Salt bridges: D:R.141 NHE.17: 8 residues within 4Å: Chain E: S.69, I.70, T.71, R.141 Chain F: P.66, M.94, A.96, F.173 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:P.66, F:A.96, F:F.173 Hydrogen bonds: E:I.70, E:T.71, E:T.71 Salt bridges: E:R.141 NHE.19: 8 residues within 4Å: Chain F: S.69, I.70, T.71, R.141, L.145 Chain G: P.66, M.94, A.96 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:P.66, G:A.96 Hydrogen bonds: F:S.69, F:I.70, F:T.71 Salt bridges: F:R.141 NHE.21: 7 residues within 4Å: Chain A: P.66, M.94, F.173 Chain G: S.69, I.70, T.71, R.141 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:P.66, A:F.173 Hydrogen bonds: G:S.69, G:I.70, G:T.71 Salt bridges: G:R.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.-G. et al., Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat.Struct.Mol.Biol. (2010)

Release Date

2010-03-23

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

ATP-dependent Clp protease proteolytic subunit

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