SMTL ID : 7fer.1

Cryo-EM structure of BsClpP-ADEP1 complex at pH 4.2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-14-mer

Ligands

14 x OTT- PHE- SER- PRO- MAA- ALA- MP8: ADEP1(Non-covalent)

OTT-PHE-SER-PRO-MAA-ALA-MP8.1: 14 residues within 4Å: Chain A: R.22, L.23, D.26, I.28, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Chain G: L.48, T.79, F.82 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:L.23, A:I.28, A:I.92, A:Y.112, G:L.48, G:F.82, G:F.82 Hydrogen bonds: A:Y.62, A:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.2: 15 residues within 4Å: Chain A: L.48, T.79, F.82 Chain B: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.23, B:I.28, B:I.92, B:Y.112, A:L.48, A:T.79, A:F.82, A:F.82 Hydrogen bonds: B:Y.62, B:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.3: 15 residues within 4Å: Chain B: L.48, T.79, F.82 Chain C: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.23, C:I.28, C:I.92, C:Y.112, B:L.48, B:F.82, B:F.82 Hydrogen bonds: C:Y.62, C:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.4: 15 residues within 4Å: Chain C: L.48, T.79, F.82 Chain D: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.48, C:F.82, D:L.23, D:I.28, D:I.92, D:Y.112 Hydrogen bonds: D:Y.62, D:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.5: 14 residues within 4Å: Chain D: L.48, T.79, F.82 Chain E: R.22, L.23, D.26, I.28, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 9 PLIP interactions: 6 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.23, E:I.28, E:I.92, E:Y.112, D:L.48, D:L.48, D:F.82 Hydrogen bonds: E:Y.62, E:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.6: 16 residues within 4Å: Chain E: V.44, L.48, T.79, F.82 Chain F: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.48, E:L.48, E:T.79, E:F.82, F:L.23, F:I.28, F:I.92, F:Y.112 Hydrogen bonds: F:Y.62, F:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.7: 14 residues within 4Å: Chain F: L.48, T.79, F.82 Chain G: R.22, L.23, D.26, I.28, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:L.48, F:F.82, F:F.82, G:L.23, G:I.28, G:I.92, G:Y.112 Hydrogen bonds: G:Y.62, G:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.8: 15 residues within 4Å: Chain H: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 Chain N: L.48, T.79, F.82 9 PLIP interactions: 6 interactions with chain H, 3 interactions with chain N Hydrophobic interactions: H:L.23, H:I.28, H:I.92, H:Y.112, N:L.48, N:F.82, N:F.82 Hydrogen bonds: H:Y.62, H:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.9: 15 residues within 4Å: Chain H: L.48, T.79, F.82 Chain I: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:L.48, H:L.48, H:F.82, H:F.82, I:L.23, I:I.28, I:I.92, I:Y.112 Hydrogen bonds: I:Y.62, I:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.10: 15 residues within 4Å: Chain I: L.48, T.79, F.82 Chain J: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 11 PLIP interactions: 6 interactions with chain J, 5 interactions with chain I Hydrophobic interactions: J:L.23, J:I.28, J:I.92, J:Y.112, I:L.48, I:L.48, I:T.79, I:F.82, I:F.82 Hydrogen bonds: J:Y.62, J:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.11: 15 residues within 4Å: Chain J: L.48, T.79, F.82 Chain K: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 9 PLIP interactions: 3 interactions with chain J, 6 interactions with chain K Hydrophobic interactions: J:L.48, J:L.48, J:F.82, K:L.23, K:I.28, K:I.92, K:Y.112 Hydrogen bonds: K:Y.62, K:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.12: 15 residues within 4Å: Chain K: L.48, T.79, F.82 Chain L: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 11 PLIP interactions: 5 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:L.48, K:L.48, K:T.79, K:F.82, K:F.82, L:L.23, L:I.28, L:I.92, L:Y.112 Hydrogen bonds: L:Y.62, L:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.13: 15 residues within 4Å: Chain L: L.48, T.79, F.82 Chain M: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 9 PLIP interactions: 6 interactions with chain M, 3 interactions with chain L Hydrophobic interactions: M:L.23, M:I.28, M:I.92, M:Y.112, L:L.48, L:F.82, L:F.82 Hydrogen bonds: M:Y.62, M:Y.62 OTT-PHE-SER-PRO-MAA-ALA-MP8.14: 15 residues within 4Å: Chain M: L.48, T.79, F.82 Chain N: R.22, L.23, D.26, I.28, S.60, Y.62, I.90, I.92, K.110, Y.112, L.114, L.189 11 PLIP interactions: 6 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:L.23, N:I.28, N:I.92, N:Y.112, M:L.48, M:L.48, M:T.79, M:F.82, M:F.82 Hydrogen bonds: N:Y.62, N:Y.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, L. et al., Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis. Embo J. (2022)

Release Date

2022-07-06

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
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit

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