SMTL ID : 8oll.2 (1 other biounit)

Staphylococcus aureus ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.7 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-14-mer

Ligands

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

VSZ.1: 12 residues within 4Å: Chain A: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.71, A:L.126, A:I.143, A:T.146 Hydrogen bonds: A:G.69, A:G.69, A:V.71, A:M.99, A:L.126, A:L.126 VSZ.2: 12 residues within 4Å: Chain B: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.71, B:L.126, B:T.146 Hydrogen bonds: B:G.69, B:G.69, B:V.71, B:M.99, B:L.126, B:L.126 Water bridges: B:S.98 VSZ.3: 13 residues within 4Å: Chain C: P.67, G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.71, C:L.126, C:I.143, C:T.146 Hydrogen bonds: C:G.69, C:G.69, C:V.71, C:M.99, C:L.126, C:L.126 VSZ.4: 12 residues within 4Å: Chain D: P.67, G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, T.146 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.71, D:L.126, D:T.146 Hydrogen bonds: D:G.69, D:V.71, D:M.99, D:L.126, D:L.126 VSZ.5: 13 residues within 4Å: Chain E: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, G.127, H.142, I.143, T.146 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:V.71, E:I.143, E:T.146 Hydrogen bonds: E:G.69, E:V.71, E:M.99, E:L.126, E:L.126, E:L.126 VSZ.6: 13 residues within 4Å: Chain F: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, G.127, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.71, F:P.125, F:I.143, F:T.146 Hydrogen bonds: F:G.69, F:G.69, F:V.71, F:M.99, F:L.126, F:L.126 VSZ.7: 12 residues within 4Å: Chain G: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:V.71, G:I.143, G:T.146 Hydrogen bonds: G:G.69, G:G.69, G:V.71, G:M.99, G:L.126, G:L.126 VSZ.8: 13 residues within 4Å: Chain H: P.67, G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:V.71, H:L.126, H:I.143, H:T.146 Hydrogen bonds: H:G.69, H:G.69, H:V.71, H:M.99, H:L.126, H:L.126 VSZ.9: 12 residues within 4Å: Chain I: P.67, G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:V.71, I:P.125, I:L.126, I:I.143 Hydrogen bonds: I:G.69, I:G.69, I:V.71, I:M.99, I:L.126, I:L.126 VSZ.10: 13 residues within 4Å: Chain J: P.67, G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, G.127, H.142, T.146 10 PLIP interactions: 10 interactions with chain J Hydrophobic interactions: J:V.71, J:L.126, J:L.126, J:T.146 Hydrogen bonds: J:G.69, J:G.69, J:V.71, J:L.126, J:L.126, J:L.126 VSZ.11: 12 residues within 4Å: Chain K: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:L.126, K:I.143, K:T.146 Hydrogen bonds: K:G.69, K:G.69, K:V.71, K:M.99, K:L.126, K:L.126 VSZ.12: 12 residues within 4Å: Chain L: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:V.71, L:L.126, L:I.143, L:T.146 Hydrogen bonds: L:G.69, L:G.69, L:V.71, L:M.99, L:L.126, L:L.126 VSZ.13: 12 residues within 4Å: Chain M: G.68, G.69, S.70, V.71, S.98, M.99, H.123, P.125, L.126, H.142, I.143, T.146 10 PLIP interactions: 10 interactions with chain M Hydrophobic interactions: M:V.71, M:L.126, M:I.143, M:T.146 Hydrogen bonds: M:G.69, M:G.69, M:V.71, M:M.99, M:L.126, M:L.126 VSZ.14: 11 residues within 4Å: Chain N: P.67, G.68, G.69, S.70, V.71, S.98, M.99, P.125, L.126, G.128, I.143 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:I.143 Hydrogen bonds: N:G.69, N:G.69, N:V.71, N:M.99, N:L.126, N:L.126

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

2023-12-06

Peptides

ATP-dependent Clp protease proteolytic subunit: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
O

B
P

C
Q

D
R

E
S

F
T

G
U

H
V

I
W

J
X

K
Y

L
Z

M
a

N
b

ATP-dependent Clp protease proteolytic subunit

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