SMTL ID : 3tt7.1

Structure of ClpP from Bacillus subtilis in complex with DFP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-14-mer

Ligands

14 x DFP: DIISOPROPYL PHOSPHONATE(Covalent)

DFP.1: 6 residues within 4Å: Chain A: G.69, S.98, M.99, H.123, L.126, L.150 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.150 Hydrogen bonds: A:G.69, A:M.99 Salt bridges: A:H.123 DFP.2: 8 residues within 4Å: Chain B: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.71, B:P.125, B:L.150 Hydrogen bonds: B:G.69, B:M.99 Salt bridges: B:H.123 DFP.3: 7 residues within 4Å: Chain C: G.69, S.98, M.99, H.123, P.125, L.126, L.150 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:P.125, C:L.126, C:L.150 Hydrogen bonds: C:G.69, C:M.99 Salt bridges: C:H.123 DFP.4: 8 residues within 4Å: Chain D: G.68, G.69, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.125, D:L.150 Hydrogen bonds: D:G.69, D:M.99 Salt bridges: D:H.123 DFP.5: 8 residues within 4Å: Chain E: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.71 Hydrogen bonds: E:G.69, E:M.99 Water bridges: E:H.123 Salt bridges: E:H.123 DFP.6: 7 residues within 4Å: Chain F: G.68, G.69, S.98, M.99, H.123, L.126, L.150 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.126, F:L.150 Hydrogen bonds: F:G.69, F:M.99 Salt bridges: F:H.123 DFP.7: 8 residues within 4Å: Chain G: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:I.71, G:P.125 Hydrogen bonds: G:G.69, G:M.99 Salt bridges: G:H.123 DFP.8: 6 residues within 4Å: Chain H: G.69, S.98, M.99, H.123, L.126, L.150 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:L.150 Hydrogen bonds: H:G.69, H:M.99 Salt bridges: H:H.123 DFP.9: 8 residues within 4Å: Chain I: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:I.71, I:P.125, I:L.150 Hydrogen bonds: I:G.69, I:M.99 Salt bridges: I:H.123 DFP.10: 7 residues within 4Å: Chain J: G.69, S.98, M.99, H.123, P.125, L.126, L.150 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:P.125, J:L.126, J:L.150 Hydrogen bonds: J:G.69, J:M.99 Salt bridges: J:H.123 DFP.11: 8 residues within 4Å: Chain K: G.68, G.69, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:P.125, K:L.150 Hydrogen bonds: K:G.69, K:M.99 Salt bridges: K:H.123 DFP.12: 8 residues within 4Å: Chain L: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:I.71 Hydrogen bonds: L:G.69, L:M.99 Water bridges: L:H.123 Salt bridges: L:H.123 DFP.13: 7 residues within 4Å: Chain M: G.68, G.69, S.98, M.99, H.123, L.126, L.150 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:L.126, M:L.150 Hydrogen bonds: M:G.69, M:M.99 Salt bridges: M:H.123 DFP.14: 8 residues within 4Å: Chain N: G.69, I.71, S.98, M.99, H.123, P.125, L.126, L.150 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:I.71, N:P.125 Hydrogen bonds: N:G.69, N:M.99 Salt bridges: N:H.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, B.-G. et al., Structural insights into the conformational diversity of ClpP from Bacillus subtilis. Mol.Cells (2011)

Release Date

2011-12-21

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit