SMTL ID : 8r05.1

Photorhabdus lamondii ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.5 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-14-mer

Ligands

14 x VSZ: Cystargolide A (bound)(Covalent)

VSZ.1: 13 residues within 4Å: Chain A: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain B: R.133 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.85, A:P.139, A:L.140, A:I.157, A:V.160 Hydrogen bonds: A:G.83, A:G.83, A:I.85, A:M.113, A:L.140, A:L.140, A:L.140 VSZ.2: 12 residues within 4Å: Chain B: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 Chain C: R.133 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.85, B:P.139, B:L.140, B:I.157 Hydrogen bonds: B:G.83, B:G.83, B:I.85, B:M.113, B:L.140, B:L.140, B:L.140 VSZ.3: 12 residues within 4Å: Chain C: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 Chain D: R.133 12 PLIP interactions: 1 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:R.133, C:G.83, C:G.83, C:I.85, C:M.113, C:L.140, C:L.140, C:L.140 Hydrophobic interactions: C:I.85, C:P.139, C:L.140, C:I.157 VSZ.4: 12 residues within 4Å: Chain D: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 Chain E: R.133 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.85, D:P.139, D:L.140, D:I.157 Hydrogen bonds: D:G.83, D:G.83, D:I.85, D:M.113, D:L.140, D:L.140, D:L.140, E:R.133 VSZ.5: 13 residues within 4Å: Chain E: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain F: R.133 13 PLIP interactions: 12 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:I.85, E:P.139, E:L.140, E:I.157, E:V.160 Hydrogen bonds: E:G.83, E:G.83, E:I.85, E:M.113, E:L.140, E:L.140, E:L.140, F:R.133 VSZ.6: 13 residues within 4Å: Chain F: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain G: R.133 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:I.85, F:P.139, F:L.140, F:I.157, F:V.160 Hydrogen bonds: F:G.83, F:G.83, F:I.85, F:M.113, F:L.140, F:L.140, F:L.140, G:R.133 VSZ.7: 13 residues within 4Å: Chain A: R.133 Chain G: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:I.85, G:P.139, G:L.140, G:I.157, G:V.160 Hydrogen bonds: G:G.83, G:G.83, G:I.85, G:M.113, G:L.140, G:L.140, G:L.140 VSZ.8: 13 residues within 4Å: Chain H: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain I: R.133 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.85, H:P.139, H:L.140, H:V.160 Hydrogen bonds: H:G.83, H:G.83, H:I.85, H:M.113, H:L.140, H:L.140 VSZ.9: 13 residues within 4Å: Chain I: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain J: R.133 12 PLIP interactions: 11 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:I.85, I:L.140, I:I.157, I:V.160 Hydrogen bonds: I:G.83, I:G.83, I:I.85, I:M.113, I:L.140, I:L.140, I:L.140, J:R.133 VSZ.10: 13 residues within 4Å: Chain J: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157, V.160 Chain K: R.133 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:I.85, J:P.139, J:I.157, J:V.160 Hydrogen bonds: J:G.83, J:G.83, J:I.85, J:M.113, J:L.140, J:L.140, J:L.140 VSZ.11: 12 residues within 4Å: Chain K: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 Chain L: R.133 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:I.85, K:L.140, K:I.157 Hydrogen bonds: K:G.83, K:G.83, K:I.85, K:M.113, K:L.140, K:L.140 VSZ.12: 12 residues within 4Å: Chain L: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 Chain M: R.133 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:I.85, L:P.139, L:I.157 Hydrogen bonds: L:G.83, L:G.83, L:I.85, L:M.113, L:L.140, L:L.140, L:L.140 VSZ.13: 11 residues within 4Å: Chain M: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, V.160 Chain N: R.133 12 PLIP interactions: 11 interactions with chain M, 1 interactions with chain N Hydrophobic interactions: M:I.85, M:I.85, M:P.139, M:L.140, M:V.160 Hydrogen bonds: M:G.83, M:G.83, M:I.85, M:M.113, M:L.140, M:L.140 Salt bridges: N:R.133 VSZ.14: 12 residues within 4Å: Chain H: R.133 Chain N: G.82, G.83, V.84, I.85, S.112, M.113, H.137, P.139, L.140, G.141, I.157 12 PLIP interactions: 11 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:I.85, N:P.139, N:L.140, N:I.157 Hydrogen bonds: N:G.83, N:G.83, N:I.85, N:M.113, N:L.140, N:L.140, N:L.140, H:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Illigmann, A. et al., Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2023-12-20

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