SMTL ID : 9g6i.1

Crystal structure of S. epidermidis ClpP in complex with bortezomib - cocrystallization

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-14-mer

Ligands

14 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 8 residues within 4Å: Chain A: S.98, S.101, F.102, M.121, I.122, H.123, L.154 Ligands: BO2.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.154 Hydrogen bonds: A:H.123 ACT.3: 7 residues within 4Å: Chain B: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.102, B:I.122, B:L.154 Hydrogen bonds: B:S.101, B:H.123 ACT.5: 7 residues within 4Å: Chain C: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.6 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.102, C:L.154 Hydrogen bonds: C:S.98, C:H.123 ACT.7: 7 residues within 4Å: Chain D: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.8 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.154 Hydrogen bonds: D:F.102, D:H.123, D:H.123 ACT.9: 7 residues within 4Å: Chain E: S.98, S.101, F.102, M.121, I.122, H.123 Ligands: BO2.10 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.102 Hydrogen bonds: E:H.123 ACT.11: 6 residues within 4Å: Chain F: S.98, S.101, F.102, I.122, H.123 Ligands: BO2.12 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:F.102, F:I.122 Hydrogen bonds: F:S.98, F:H.123 ACT.13: 8 residues within 4Å: Chain G: S.98, S.101, F.102, M.121, I.122, H.123, L.154 Ligands: BO2.14 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.102, G:I.122 Hydrogen bonds: G:S.101, G:H.123 ACT.15: 8 residues within 4Å: Chain H: S.98, S.101, F.102, M.121, I.122, H.123, L.154 Ligands: BO2.16 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:L.154 Hydrogen bonds: H:S.98, H:S.101, H:H.123 ACT.17: 8 residues within 4Å: Chain I: S.98, S.101, F.102, I.122, H.123, L.154, T.169 Ligands: BO2.18 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:L.154, I:T.169 Hydrogen bonds: I:H.123 ACT.19: 7 residues within 4Å: Chain J: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.20 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:I.122 Hydrogen bonds: J:H.123 ACT.21: 7 residues within 4Å: Chain K: S.98, S.101, F.102, M.121, I.122, H.123 Ligands: BO2.22 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:H.123 ACT.23: 7 residues within 4Å: Chain L: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.24 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:L.154 Hydrogen bonds: L:H.123, L:H.123 ACT.25: 7 residues within 4Å: Chain M: S.98, S.101, F.102, I.122, H.123, L.154 Ligands: BO2.26 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:L.154 Hydrogen bonds: M:F.102, M:H.123, M:H.123 ACT.27: 9 residues within 4Å: Chain N: S.98, S.101, F.102, M.121, I.122, H.123, L.154, T.169 Ligands: BO2.28 6 PLIP interactions: 6 interactions with chain N Hydrophobic interactions: N:L.154, N:T.169 Hydrogen bonds: N:S.98, N:S.101, N:H.123, N:H.123

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

BO2.2: 14 residues within 4Å: Chain A: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.71, A:M.99, A:L.150, A:L.150 Hydrogen bonds: A:G.69, A:G.69, A:G.69, A:V.71, A:M.99, A:L.126, A:L.126 Water bridges: A:T.72, A:I.143, A:T.146 BO2.4: 14 residues within 4Å: Chain B: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.3 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.71, B:M.99, B:P.125, B:L.150 Hydrogen bonds: B:G.69, B:G.69, B:G.69, B:V.71, B:M.99, B:L.126, B:L.126 Water bridges: B:G.128, B:I.143, B:T.146 BO2.6: 13 residues within 4Å: Chain C: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143 Ligands: ACT.5 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.71, C:M.99 Hydrogen bonds: C:G.69, C:G.69, C:G.69, C:V.71, C:M.99, C:L.126, C:L.126 Water bridges: C:T.72, C:I.143, C:T.146 BO2.8: 14 residues within 4Å: Chain D: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.71, D:M.99, D:L.150 Hydrogen bonds: D:G.69, D:G.69, D:G.69, D:V.71, D:M.99, D:L.126, D:L.126, D:T.146 BO2.10: 14 residues within 4Å: Chain E: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.9 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:V.71, E:M.99, E:P.125 Hydrogen bonds: E:G.69, E:G.69, E:G.69, E:V.71, E:M.99, E:L.126, E:L.126 Water bridges: E:I.143 BO2.12: 14 residues within 4Å: Chain F: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.11 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:V.71, F:M.99, F:P.125, F:L.150 Hydrogen bonds: F:G.69, F:G.69, F:G.69, F:V.71, F:M.99, F:L.126, F:L.126 BO2.14: 15 residues within 4Å: Chain G: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, H.142, I.143, L.150 Ligands: ACT.13 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:V.71, G:M.99, G:P.125, G:L.150 Hydrogen bonds: G:G.69, G:G.69, G:G.69, G:V.71, G:M.99, G:L.126, G:L.126 Water bridges: G:I.143 BO2.16: 13 residues within 4Å: Chain H: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143 Ligands: ACT.15 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:V.71, H:M.99 Hydrogen bonds: H:G.69, H:G.69, H:G.69, H:V.71, H:M.99, H:L.126, H:L.126 BO2.18: 14 residues within 4Å: Chain I: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.17 12 PLIP interactions: 12 interactions with chain I Hydrophobic interactions: I:V.71, I:M.99, I:L.150 Hydrogen bonds: I:G.69, I:G.69, I:G.69, I:V.71, I:M.99, I:L.126, I:L.126 Water bridges: I:T.72, I:I.143 BO2.20: 13 residues within 4Å: Chain J: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143 Ligands: ACT.19 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:V.71, J:M.99 Hydrogen bonds: J:G.69, J:G.69, J:G.69, J:V.71, J:M.99, J:L.126, J:L.126 Water bridges: J:T.72, J:I.143 BO2.22: 14 residues within 4Å: Chain K: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, H.142, I.143 Ligands: ACT.21 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:V.71, K:M.99 Hydrogen bonds: K:G.69, K:G.69, K:G.69, K:V.71, K:M.99, K:L.126, K:L.126 Water bridges: K:T.72, K:I.143 BO2.24: 14 residues within 4Å: Chain L: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143, L.150 Ligands: ACT.23 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:V.71, L:M.99, L:P.125, L:L.150, L:L.150 Hydrogen bonds: L:G.69, L:G.69, L:G.69, L:V.71, L:M.99, L:L.126, L:L.126 Water bridges: L:T.72, L:T.146 BO2.26: 13 residues within 4Å: Chain M: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, H.142, I.143 Ligands: ACT.25 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:V.71, M:M.99 Hydrogen bonds: M:G.69, M:G.69, M:G.69, M:V.71, M:M.99, M:L.126, M:L.126 Water bridges: M:I.143, M:T.146 BO2.28: 14 residues within 4Å: Chain N: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, H.142, I.143 Ligands: ACT.27 10 PLIP interactions: 10 interactions with chain N Hydrophobic interactions: N:V.71, N:M.99 Hydrogen bonds: N:G.69, N:G.69, N:G.69, N:V.71, N:M.99, N:L.126, N:L.126 Water bridges: N:I.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alves Franca, B. et al., Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds. Sci Rep (2024)

Release Date

2025-07-30

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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