SMTL ID : 3ktj.1

Structure of ClpP in complex with ADEP2 in monoclinic crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-heptamer

Ligands

7 x CXP- WFP- SER- PRO- YCP- ALA- MP8: Acyldepsipeptide 2(Non-covalent)

CXP-WFP-SER-PRO-YCP-ALA-MP8.1: 18 residues within 4Å: Chain A: V.44, L.48, F.49, A.52, D.78, T.79, F.82, K.84 Chain B: L.23, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.2: 16 residues within 4Å: Chain A: R.22, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Chain G: V.44, L.48, F.49, D.78, T.79, F.82 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.3: 16 residues within 4Å: Chain E: V.44, L.48, F.49, A.52, D.78, T.79, F.82 Chain F: D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.4: 17 residues within 4Å: Chain B: V.44, L.48, F.49, A.52, T.79, F.82 Chain C: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.5: 15 residues within 4Å: Chain C: V.44, L.48, D.78, T.79, F.82 Chain D: L.23, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.6: 18 residues within 4Å: Chain D: V.44, L.48, F.49, A.52, D.78, T.79, F.82, K.84 Chain E: L.23, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available CXP-WFP-SER-PRO-YCP-ALA-MP8.7: 15 residues within 4Å: Chain F: V.44, L.48, A.52, T.79, F.82 Chain G: L.23, D.26, I.28, S.60, Y.62, I.90, I.92, Y.112, L.114, L.189 Protein-ligand interaction information (PLIP) not available

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

NHE.8: 6 residues within 4Å: Chain A: S.69, I.70, T.71, R.141 Chain B: P.66, M.94 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.66 Hydrogen bonds: A:I.70, A:T.71, A:T.71 Salt bridges: A:R.141 NHE.9: 7 residues within 4Å: Chain B: S.69, I.70, T.71, R.141 Chain C: P.66, M.94, F.173 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:I.70, B:T.71 Water bridges: B:T.71, B:L.125 Salt bridges: B:R.141 Hydrophobic interactions: C:P.66, C:F.173 NHE.10: 6 residues within 4Å: Chain C: S.69, I.70, T.71, R.141 Chain D: P.66, M.94 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.69, C:I.70, C:T.71 Water bridges: C:R.141 Salt bridges: C:R.141 Hydrophobic interactions: D:P.66 NHE.11: 6 residues within 4Å: Chain D: I.70, T.71, R.141 Chain E: P.66, M.94, F.173 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:P.66, E:F.173 Hydrogen bonds: D:I.70, D:T.71 Water bridges: D:L.125 Salt bridges: D:R.141 NHE.12: 6 residues within 4Å: Chain E: S.69, I.70, T.71, R.141 Chain F: P.66, M.94 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:I.70, E:T.71 Water bridges: E:L.125 Salt bridges: E:R.141 Hydrophobic interactions: F:P.66 NHE.13: 7 residues within 4Å: Chain F: S.69, I.70, T.71, R.141, L.145 Chain G: P.66, M.94 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:S.69, F:I.70, F:T.71 Water bridges: F:S.69, F:T.71 Salt bridges: F:R.141 Hydrophobic interactions: G:P.66 NHE.14: 4 residues within 4Å: Chain G: S.69, I.70, T.71, R.141 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.69, G:I.70, G:T.71 Water bridges: G:S.69 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

Related Entries With Identical Sequence