SMTL ID : 3mt6.2 (1 other biounit)

Structure of ClpP from Escherichia coli in complex with ADEP1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

14 x OTT- PHE- SER- PRO- MAA- ALA- MP8: ACYLDEPSIPEPTIDE 1(Non-covalent)

OTT-PHE-SER-PRO-MAA-ALA-MP8.1: 18 residues within 4Å: Chain M: R.36, L.37, E.40, V.42, Y.74, Y.76, S.102, I.104, M.106, F.126, L.128, L.203, R.206 Chain N: L.62, E.65, A.66, T.93, F.96 18 PLIP interactions: 14 interactions with chain M, 4 interactions with chain N Hydrophobic interactions: M:R.36, M:L.37, M:E.40, M:V.42, M:Y.74, M:Y.74, M:Y.76, M:F.126, M:L.128, M:L.203, N:L.62, N:L.62, N:F.96 Hydrogen bonds: M:Y.74, M:Y.76, M:Y.76 Water bridges: M:S.102 pi-Stacking: N:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.2: 16 residues within 4Å: Chain L: R.36, L.37, E.40, V.42, Y.74, Y.76, S.102, I.104, M.106, F.126, L.128, L.203 Chain M: L.62, A.66, T.93, F.96 18 PLIP interactions: 15 interactions with chain L, 3 interactions with chain M Hydrophobic interactions: L:R.36, L:L.37, L:E.40, L:V.42, L:Y.74, L:Y.76, L:I.104, L:F.126, L:L.128, L:L.128, L:L.203, M:L.62 Hydrogen bonds: L:Y.74, L:Y.76, L:Y.76, M:E.65 Water bridges: L:S.102 pi-Stacking: M:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.3: 16 residues within 4Å: Chain K: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, L.128, L.203 Chain L: L.62, F.63, E.65, A.66, T.93, F.96 18 PLIP interactions: 14 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:R.36, K:L.37, K:E.40, K:E.40, K:V.42, K:Y.74, K:Y.76, K:I.104, K:L.128, K:L.128, K:L.203, L:F.63, L:F.96 Hydrogen bonds: K:Y.74, K:Y.76, K:Y.76, L:E.65 pi-Stacking: L:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.4: 16 residues within 4Å: Chain J: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, F.126, L.128, L.203 Chain K: L.62, E.65, A.66, T.93, F.96 15 PLIP interactions: 12 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:R.36, J:L.37, J:E.40, J:V.42, J:Y.74, J:Y.76, J:F.126, J:L.128, J:L.203, K:L.62, K:F.96 Hydrogen bonds: J:Y.74, J:Y.76, J:Y.76 pi-Stacking: K:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.5: 17 residues within 4Å: Chain I: R.36, L.37, E.40, V.42, Y.74, Y.76, S.102, I.104, M.106, F.126, L.203 Chain J: V.58, L.62, F.63, A.66, T.93, F.96 13 PLIP interactions: 10 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:R.36, I:L.37, I:V.42, I:Y.74, I:Y.76, I:F.126, I:L.203, J:V.58, J:F.63, J:F.96 Hydrogen bonds: I:Y.76, I:Y.76 Water bridges: I:Y.74 OTT-PHE-SER-PRO-MAA-ALA-MP8.6: 15 residues within 4Å: Chain H: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, L.128, L.203 Chain I: L.62, F.63, A.66, T.93, F.96 17 PLIP interactions: 14 interactions with chain H, 3 interactions with chain I Hydrophobic interactions: H:R.36, H:L.37, H:E.40, H:E.40, H:V.42, H:Y.74, H:Y.76, H:I.104, H:L.128, H:L.128, H:L.203, I:F.63, I:F.96 Hydrogen bonds: H:Y.76, H:Y.76 Water bridges: H:S.102 pi-Stacking: I:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.7: 16 residues within 4Å: Chain H: L.62, E.65, A.66, T.93, F.96 Chain N: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, F.126, L.128, L.203 17 PLIP interactions: 13 interactions with chain N, 4 interactions with chain H Hydrophobic interactions: N:R.36, N:L.37, N:E.40, N:V.42, N:Y.74, N:Y.76, N:F.126, N:L.128, N:L.203, H:L.62, H:L.62, H:F.96 Hydrogen bonds: N:Y.74, N:Y.76, N:Y.76 Water bridges: N:S.102 pi-Stacking: H:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.8: 16 residues within 4Å: Chain E: L.62, A.66, T.93, F.96 Chain F: R.36, L.37, E.40, V.42, Y.74, Y.76, S.102, I.104, M.106, F.126, L.128, L.203 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:R.36, F:L.37, F:V.42, F:Y.74, F:Y.74, F:Y.76, F:F.126, F:L.128, F:L.128, F:L.203, E:F.96 Hydrogen bonds: F:Y.74, F:Y.76, F:Y.76 Water bridges: F:S.102, E:E.65 pi-Stacking: E:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.9: 14 residues within 4Å: Chain D: L.62, A.66, T.93, F.96 Chain E: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, L.128, L.203 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:R.36, E:L.37, E:E.40, E:V.42, E:Y.74, E:Y.76, E:I.104, E:L.128, E:L.203, D:L.62 Hydrogen bonds: E:Y.76, E:Y.76 Water bridges: E:S.102 pi-Stacking: D:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.10: 16 residues within 4Å: Chain C: L.62, F.63, A.66, T.93, F.96 Chain D: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, F.126, L.128, L.203 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:R.36, D:L.37, D:E.40, D:V.42, D:Y.74, D:Y.76, D:F.126, D:L.128, D:L.128, D:L.203, C:L.62, C:F.63, C:F.96 Hydrogen bonds: D:Y.76, D:Y.76 Water bridges: D:S.102 pi-Stacking: C:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.11: 15 residues within 4Å: Chain B: L.62, A.66, T.93, F.96 Chain C: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, F.126, L.128, L.203 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:R.36, C:L.37, C:V.42, C:Y.74, C:Y.76, C:I.104, C:F.126, C:L.128, C:L.203, B:F.96 Hydrogen bonds: C:Y.76, C:Y.76 Water bridges: C:S.102 pi-Stacking: B:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.12: 15 residues within 4Å: Chain A: L.62, F.63, A.66, T.93, F.96 Chain B: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, L.128, L.203 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:R.36, B:L.37, B:E.40, B:V.42, B:Y.74, B:Y.76, B:I.104, B:L.128, B:L.128, B:L.203, A:F.63, A:F.96 Hydrogen bonds: B:Y.76, B:Y.76 pi-Stacking: A:F.96 OTT-PHE-SER-PRO-MAA-ALA-MP8.13: 15 residues within 4Å: Chain A: R.36, L.37, E.40, V.42, Y.74, Y.76, I.104, M.106, L.128, L.203 Chain G: L.62, F.63, A.66, T.93, F.96 17 PLIP interactions: 4 interactions with chain G, 13 interactions with chain A Hydrophobic interactions: G:L.62, G:F.63, G:F.96, A:R.36, A:L.37, A:E.40, A:E.40, A:V.42, A:Y.74, A:Y.74, A:Y.76, A:I.104, A:L.128, A:L.203 Hydrogen bonds: G:E.65, A:Y.76, A:Y.76 OTT-PHE-SER-PRO-MAA-ALA-MP8.14: 14 residues within 4Å: Chain F: L.62, A.66, T.93, F.96 Chain G: R.36, E.40, V.42, Y.74, Y.76, I.104, M.106, F.126, L.128, L.203 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:R.36, G:E.40, G:V.42, G:Y.74, G:Y.76, G:F.126, G:L.128, G:L.203, F:L.62, F:F.96 Hydrogen bonds: G:Y.76, G:Y.76 Water bridges: G:Y.74, G:S.102, F:E.65 pi-Stacking: F:F.96

28 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.15: 8 residues within 4Å: Chain A: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.16: 6 residues within 4Å: Chain A: N.130, R.132 Chain G: E.155, K.158, V.159, R.162 Ligand excluded by PLIP MPD.17: 6 residues within 4Å: Chain A: E.155, K.158, V.159, R.162 Chain B: N.130, R.132 Ligand excluded by PLIP MPD.18: 8 residues within 4Å: Chain B: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.19: 7 residues within 4Å: Chain B: E.155, K.158, V.159, R.162 Chain C: N.130, R.132, S.189 Ligand excluded by PLIP MPD.20: 8 residues within 4Å: Chain C: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.21: 5 residues within 4Å: Chain C: K.158, R.162 Chain D: N.130, R.132, S.189 Ligand excluded by PLIP MPD.22: 8 residues within 4Å: Chain D: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.167 Ligand excluded by PLIP MPD.23: 5 residues within 4Å: Chain D: K.158, V.159, R.162 Chain E: N.130, R.132 Ligand excluded by PLIP MPD.24: 9 residues within 4Å: Chain E: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.25: 4 residues within 4Å: Chain E: K.158, R.162 Chain F: N.130, R.132 Ligand excluded by PLIP MPD.26: 9 residues within 4Å: Chain F: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.27: 9 residues within 4Å: Chain G: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.28: 5 residues within 4Å: Chain F: K.158, R.162 Chain G: N.130, R.132, S.189 Ligand excluded by PLIP MPD.29: 9 residues within 4Å: Chain H: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.30: 6 residues within 4Å: Chain H: N.130, R.132, S.189 Chain I: E.155, K.158, R.162 Ligand excluded by PLIP MPD.31: 9 residues within 4Å: Chain I: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.32: 5 residues within 4Å: Chain I: N.130, R.132, S.189 Chain J: K.158, R.162 Ligand excluded by PLIP MPD.33: 8 residues within 4Å: Chain J: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.34: 7 residues within 4Å: Chain J: N.130, R.132, S.189 Chain K: E.155, K.158, V.159, R.162 Ligand excluded by PLIP MPD.35: 8 residues within 4Å: Chain K: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.36: 4 residues within 4Å: Chain K: N.130, R.132 Chain L: K.158, R.162 Ligand excluded by PLIP MPD.37: 9 residues within 4Å: Chain L: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.38: 4 residues within 4Å: Chain L: N.130, R.132 Chain M: K.158, R.162 Ligand excluded by PLIP MPD.39: 8 residues within 4Å: Chain M: S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.40: 4 residues within 4Å: Chain M: N.130, R.132 Chain N: K.158, R.162 Ligand excluded by PLIP MPD.41: 9 residues within 4Å: Chain N: I.84, S.111, M.112, I.135, H.136, Q.137, P.138, M.163, M.167 Ligand excluded by PLIP MPD.42: 6 residues within 4Å: Chain H: E.155, K.158, V.159, R.162 Chain N: N.130, R.132 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D.H. et al., Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP. Chem.Biol. (2010)

Release Date

2010-11-03

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
L

C
K

D
J

E
I

F
H

G
N

H
F

I
E

J
D

K
C

L
B

M
A

N
G

ATP-dependent Clp protease proteolytic subunit

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