SMTL ID : 9dql.1

human ClpP - Bortezomib - A192E / E196R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-14-mer

Ligands

14 x BO2: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE(Covalent)

BO2.1: 16 residues within 4Å: Chain A: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 Chain G: R.174 Chain H: R.185 11 PLIP interactions: 2 interactions with chain G, 9 interactions with chain A Hydrogen bonds: G:R.174, G:R.174, A:G.124, A:G.124, A:G.124, A:V.126, A:M.154, A:S.181, A:S.181 Hydrophobic interactions: A:V.126, A:L.205 BO2.4: 16 residues within 4Å: Chain A: R.174 Chain B: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 Chain N: R.185 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.126, B:L.205 Hydrogen bonds: B:G.124, B:G.124, B:G.124, B:V.126, B:M.154, B:S.181, B:S.181, A:R.174, A:R.174 BO2.5: 15 residues within 4Å: Chain B: R.174 Chain C: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.126, C:L.205 Hydrogen bonds: C:G.124, C:G.124, C:G.124, C:G.124, C:V.126, C:M.154, C:S.181, C:S.181, B:R.174, B:R.174 BO2.7: 15 residues within 4Å: Chain C: R.174 Chain D: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.126, D:L.205 Hydrogen bonds: D:G.124, D:G.124, D:G.124, D:G.124, D:V.126, D:M.154, D:S.181, D:S.181, C:R.174, C:R.174 BO2.8: 16 residues within 4Å: Chain D: R.174 Chain E: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 Chain K: R.185 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:V.126, E:L.205 Hydrogen bonds: E:G.124, E:G.124, E:G.124, E:V.126, E:M.154, E:S.181, E:S.181, D:R.174, D:R.174 BO2.9: 14 residues within 4Å: Chain E: R.174 Chain F: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.205 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:V.125, F:L.205 Hydrogen bonds: F:G.124, F:G.124, F:G.124, F:V.126, F:M.154, F:S.181, F:S.181, E:R.174, E:R.174 BO2.11: 15 residues within 4Å: Chain F: R.174 Chain G: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 11 PLIP interactions: 10 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:V.126, G:L.205 Hydrogen bonds: G:G.124, G:G.124, G:G.124, G:G.124, G:V.126, G:M.154, G:S.181, G:S.181, F:R.174 BO2.13: 15 residues within 4Å: Chain H: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 Chain N: R.174 11 PLIP interactions: 2 interactions with chain N, 9 interactions with chain H Hydrogen bonds: N:R.174, N:R.174, H:G.124, H:G.124, H:G.124, H:V.126, H:M.154, H:S.181, H:S.181 Hydrophobic interactions: H:V.125, H:L.205 BO2.15: 14 residues within 4Å: Chain H: R.174 Chain I: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, L.201, L.205 10 PLIP interactions: 8 interactions with chain I, 2 interactions with chain H Hydrophobic interactions: I:V.126, I:L.205 Hydrogen bonds: I:G.124, I:G.124, I:V.126, I:M.154, I:S.181, I:S.181, H:R.174, H:R.174 BO2.17: 15 residues within 4Å: Chain I: R.174 Chain J: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 13 PLIP interactions: 12 interactions with chain J, 1 interactions with chain I Hydrophobic interactions: J:V.125, J:V.125, J:V.126, J:L.205 Hydrogen bonds: J:G.124, J:G.124, J:G.124, J:G.124, J:V.126, J:M.154, J:S.181, J:S.181, I:R.174 BO2.18: 16 residues within 4Å: Chain E: R.185 Chain J: R.174 Chain K: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 12 PLIP interactions: 10 interactions with chain K, 2 interactions with chain J Hydrophobic interactions: K:V.126, K:L.205 Hydrogen bonds: K:G.124, K:G.124, K:G.124, K:G.124, K:V.126, K:M.154, K:S.181, K:S.181, J:R.174, J:R.174 BO2.19: 15 residues within 4Å: Chain K: R.174 Chain L: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.201, L.205 12 PLIP interactions: 10 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:V.126, L:L.205 Hydrogen bonds: L:G.124, L:G.124, L:G.124, L:G.124, L:V.126, L:M.154, L:S.181, L:S.181, K:R.174, K:R.174 BO2.21: 14 residues within 4Å: Chain L: R.174 Chain M: G.123, G.124, V.125, V.126, S.153, M.154, H.178, P.180, S.181, G.182, I.198, L.201, L.205 13 PLIP interactions: 11 interactions with chain M, 2 interactions with chain L Hydrophobic interactions: M:V.126, M:M.154, M:L.205, M:L.205 Hydrogen bonds: M:G.124, M:G.124, M:G.124, M:V.126, M:M.154, M:S.181, M:S.181, L:R.174, L:R.174 BO2.22: 13 residues within 4Å: Chain N: G.123, G.124, V.125, V.126, S.153, M.154, H.178, Q.179, P.180, S.181, G.182, I.198, L.205 11 PLIP interactions: 10 interactions with chain N, 1 interactions with chain M Hydrophobic interactions: N:V.126, N:L.205 Hydrogen bonds: N:G.124, N:G.124, N:G.124, N:G.124, N:V.126, N:M.154, N:S.181, N:S.181, M:R.174

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: D.134, Q.137 Chain G: P.171 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: M.136, I.139, N.141 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: M.136, I.139, N.141 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain F: M.136, I.139, N.141, I.143 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain G: M.136, I.139, N.141 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain H: M.136, I.139, N.141 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain I: M.136, I.139, N.141 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain L: M.136, I.139, N.141 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain N: M.136, Q.137, I.139, N.141 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goncalves, M.M. et al., Mechanism of allosteric activation in human mitochondrial ClpP protease. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-04-30

Peptides

ATP-dependent Clp protease proteolytic subunit, mitochondrial: 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, mitochondrial

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