SMTL ID : 6hwn.1

Structure of Thermus thermophilus ClpP in complex with a tripeptide.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-14-mer

Ligands

14 x UNK- UNK- UNK: Unknown tripeptide(Non-covalent)

UNK-UNK-UNK.1: 10 residues within 4Å: Chain A: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125, I.142 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.142 Hydrogen bonds: A:G.68, A:G.68, A:V.70, A:S.97, A:M.98, A:W.125, A:W.125 Water bridges: A:D.71, A:D.71 Salt bridges: A:H.122 UNK-UNK-UNK.2: 9 residues within 4Å: Chain B: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.70 Hydrogen bonds: B:G.68, B:G.68, B:V.70, B:S.97, B:M.98, B:W.125, B:W.125 Water bridges: B:D.71 Salt bridges: B:H.122 UNK-UNK-UNK.3: 9 residues within 4Å: Chain C: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.70 Hydrogen bonds: C:G.68, C:G.68, C:V.70, C:S.97, C:M.98, C:W.125, C:W.125 Water bridges: C:D.71 Salt bridges: C:H.122 UNK-UNK-UNK.4: 9 residues within 4Å: Chain D: G.67, G.68, E.69, V.70, S.97, M.98, P.124, W.125, I.142 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.70 Hydrogen bonds: D:G.68, D:G.68, D:V.70, D:S.97, D:M.98, D:W.125, D:W.125 Water bridges: D:D.71 UNK-UNK-UNK.5: 9 residues within 4Å: Chain E: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.70, E:W.125 Hydrogen bonds: E:G.68, E:G.68, E:V.70, E:S.97, E:M.98, E:W.125, E:W.125, E:W.125 Water bridges: E:D.71 Salt bridges: E:H.122 UNK-UNK-UNK.6: 10 residues within 4Å: Chain F: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125, I.142 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.70 Hydrogen bonds: F:G.68, F:G.68, F:V.70, F:S.97, F:M.98, F:W.125, F:W.125 Water bridges: F:D.71 Salt bridges: F:H.122 UNK-UNK-UNK.7: 9 residues within 4Å: Chain G: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:G.68, G:G.68, G:V.70, G:S.97, G:M.98, G:W.125, G:W.125 Water bridges: G:D.71 Salt bridges: G:H.122 UNK-UNK-UNK.25: 10 residues within 4Å: Chain H: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125, I.142 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.142 Hydrogen bonds: H:G.68, H:G.68, H:V.70, H:S.97, H:M.98, H:W.125, H:W.125 Water bridges: H:D.71 Salt bridges: H:H.122 UNK-UNK-UNK.26: 9 residues within 4Å: Chain I: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:V.70 Hydrogen bonds: I:G.68, I:G.68, I:G.68, I:V.70, I:S.97, I:M.98, I:W.125, I:W.125, I:W.125 Water bridges: I:D.71 Salt bridges: I:H.122 UNK-UNK-UNK.27: 9 residues within 4Å: Chain J: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:V.70 Hydrogen bonds: J:G.68, J:G.68, J:V.70, J:S.97, J:M.98, J:W.125, J:W.125 Water bridges: J:D.71 Salt bridges: J:H.122 UNK-UNK-UNK.28: 9 residues within 4Å: Chain K: G.67, G.68, E.69, V.70, S.97, M.98, P.124, W.125, I.142 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.70 Hydrogen bonds: K:G.68, K:G.68, K:V.70, K:S.97, K:M.98, K:W.125, K:W.125 Water bridges: K:D.71 UNK-UNK-UNK.29: 9 residues within 4Å: Chain L: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:V.70, L:W.125 Hydrogen bonds: L:G.68, L:G.68, L:V.70, L:S.97, L:M.98, L:W.125, L:W.125 Water bridges: L:D.71 Salt bridges: L:H.122 UNK-UNK-UNK.30: 10 residues within 4Å: Chain M: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125, I.142 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:V.70 Hydrogen bonds: M:G.68, M:G.68, M:V.70, M:S.97, M:M.98, M:W.125, M:W.125 Water bridges: M:D.71 Salt bridges: M:H.122 UNK-UNK-UNK.31: 9 residues within 4Å: Chain N: G.67, G.68, E.69, V.70, S.97, M.98, H.122, P.124, W.125 9 PLIP interactions: 9 interactions with chain N Hydrogen bonds: N:G.68, N:G.68, N:V.70, N:S.97, N:M.98, N:W.125, N:W.125 Water bridges: N:D.71 Salt bridges: N:H.122

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

PEG.8: 4 residues within 4Å: Chain A: T.157, Q.159, E.181, Y.182 Ligand excluded by PLIP PEG.9: 5 residues within 4Å: Chain A: Y.172, L.174, E.178, E.181, Y.182 Ligand excluded by PLIP PEG.10: 4 residues within 4Å: Chain A: N.56, E.58, P.86, R.110 Ligand excluded by PLIP PEG.11: 7 residues within 4Å: Chain B: T.157, G.158, Q.159, E.181, Y.182, G.183 Ligands: PEG.12 Ligand excluded by PLIP PEG.12: 7 residues within 4Å: Chain B: K.108, R.111, H.156, T.157, G.158, G.183 Ligands: PEG.11 Ligand excluded by PLIP PEG.13: 2 residues within 4Å: Chain B: Y.172, Y.173 Ligand excluded by PLIP PEG.14: 1 residues within 4Å: Chain C: Q.140 Ligand excluded by PLIP PEG.15: 5 residues within 4Å: Chain C: K.108, H.156, T.157, G.158 Ligands: PEG.16 Ligand excluded by PLIP PEG.16: 7 residues within 4Å: Chain C: T.157, G.158, L.180, E.181, Y.182, G.183 Ligands: PEG.15 Ligand excluded by PLIP PEG.17: 7 residues within 4Å: Chain D: T.157, G.158, Q.159, E.181, Y.182, G.183 Ligands: PEG.20 Ligand excluded by PLIP PEG.18: 7 residues within 4Å: Chain D: Y.77, D.78, Q.81, F.82 Chain E: P.115, H.116, T.190 Ligand excluded by PLIP PEG.19: 6 residues within 4Å: Chain D: P.115, S.175, A.176, Q.177, E.178, V.188 Ligand excluded by PLIP PEG.20: 5 residues within 4Å: Chain D: K.108, H.156, T.157, G.158 Ligands: PEG.17 Ligand excluded by PLIP PEG.21: 2 residues within 4Å: Chain E: Y.172, Y.173 Ligand excluded by PLIP PEG.22: 4 residues within 4Å: Chain E: Q.81, K.155, H.156 Chain F: R.191 Ligand excluded by PLIP PEG.23: 3 residues within 4Å: Chain F: P.34, I.35, G.68 Ligand excluded by PLIP PEG.24: 5 residues within 4Å: Chain G: T.157, G.158, Q.159, E.181, Y.182 Ligand excluded by PLIP PEG.32: 4 residues within 4Å: Chain H: T.157, Q.159, E.181, Y.182 Ligand excluded by PLIP PEG.33: 5 residues within 4Å: Chain H: Y.172, L.174, E.178, E.181, Y.182 Ligand excluded by PLIP PEG.34: 4 residues within 4Å: Chain H: N.56, E.58, P.86, R.110 Ligand excluded by PLIP PEG.35: 7 residues within 4Å: Chain I: T.157, G.158, Q.159, E.181, Y.182, G.183 Ligands: PEG.36 Ligand excluded by PLIP PEG.36: 7 residues within 4Å: Chain I: K.108, R.111, H.156, T.157, G.158, G.183 Ligands: PEG.35 Ligand excluded by PLIP PEG.37: 2 residues within 4Å: Chain I: Y.172, Y.173 Ligand excluded by PLIP PEG.38: 1 residues within 4Å: Chain J: Q.140 Ligand excluded by PLIP PEG.39: 5 residues within 4Å: Chain J: K.108, H.156, T.157, G.158 Ligands: PEG.40 Ligand excluded by PLIP PEG.40: 7 residues within 4Å: Chain J: T.157, G.158, L.180, E.181, Y.182, G.183 Ligands: PEG.39 Ligand excluded by PLIP PEG.41: 7 residues within 4Å: Chain K: T.157, G.158, Q.159, E.181, Y.182, G.183 Ligands: PEG.44 Ligand excluded by PLIP PEG.42: 7 residues within 4Å: Chain K: Y.77, D.78, Q.81, F.82 Chain L: P.115, H.116, T.190 Ligand excluded by PLIP PEG.43: 6 residues within 4Å: Chain K: P.115, S.175, A.176, Q.177, E.178, V.188 Ligand excluded by PLIP PEG.44: 5 residues within 4Å: Chain K: K.108, H.156, T.157, G.158 Ligands: PEG.41 Ligand excluded by PLIP PEG.45: 2 residues within 4Å: Chain L: Y.172, Y.173 Ligand excluded by PLIP PEG.46: 4 residues within 4Å: Chain L: Q.81, K.155, H.156 Chain M: R.191 Ligand excluded by PLIP PEG.47: 3 residues within 4Å: Chain M: P.34, I.35, G.68 Ligand excluded by PLIP PEG.48: 5 residues within 4Å: Chain N: T.157, G.158, Q.159, E.181, Y.182 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Felix, J. et al., Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Sci Adv (2019)

Release Date

2019-09-18

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

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