SMTL ID : 6pka.1

Structure of ClpP from Staphylococcus aureus in complex with ureadepsipeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-14-mer

Ligands

14 x OO1- WFP- SER- PRO- YCP- ALA- MP8: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide(Non-covalent)

OO1-WFP-SER-PRO-YCP-ALA-MP8.1: 17 residues within 4Å: Chain A: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 Chain B: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.24, A:D.27, A:I.29, A:Y.61, A:I.91, A:L.115, B:L.49, B:L.49, B:A.53 Hydrogen bonds: A:Y.63, A:Y.63, A:Y.63, A:Q.89, B:Q.52 Halogen bonds: B:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.2: 18 residues within 4Å: Chain B: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain C: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 18 PLIP interactions: 5 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:L.49, C:L.49, C:A.53, B:L.24, B:D.27, B:I.29, B:Y.61, B:Y.61, B:Y.63, B:I.91, B:F.113, B:L.115 Hydrogen bonds: C:Q.52, B:Y.63, B:Y.63, B:Y.63, B:Q.89 Halogen bonds: C:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.3: 16 residues within 4Å: Chain C: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain D: V.45, L.49, A.53, T.80, H.83 19 PLIP interactions: 13 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.24, C:D.27, C:I.29, C:Y.61, C:Y.61, C:Y.63, C:I.91, C:F.113, C:L.115, D:L.49, D:A.53 Hydrogen bonds: C:Y.63, C:Y.63, C:Y.63, C:Q.89 Water bridges: D:Q.52, D:Q.52, D:H.83 pi-Stacking: D:H.83 OO1-WFP-SER-PRO-YCP-ALA-MP8.4: 17 residues within 4Å: Chain D: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 Chain E: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 18 PLIP interactions: 5 interactions with chain E, 13 interactions with chain D Hydrophobic interactions: E:L.49, E:L.49, E:A.53, D:L.24, D:D.27, D:I.29, D:Y.61, D:Y.61, D:Y.63, D:I.91, D:L.115 Hydrogen bonds: E:Q.52, D:Y.63, D:Y.63, D:Y.63, D:Q.89 Halogen bonds: E:D.79 Water bridges: D:Y.61 OO1-WFP-SER-PRO-YCP-ALA-MP8.5: 17 residues within 4Å: Chain E: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain F: V.45, L.49, A.53, D.79, T.80, H.83 18 PLIP interactions: 13 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:L.24, E:D.27, E:I.29, E:Y.61, E:Y.61, E:Y.63, E:I.91, E:F.113, E:L.115, F:L.49, F:A.53 Hydrogen bonds: E:Y.63, E:Y.63, E:Y.63, E:Q.89, F:Q.52 Water bridges: F:H.83 Halogen bonds: F:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.6: 18 residues within 4Å: Chain F: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain G: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 17 PLIP interactions: 11 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:L.24, F:D.27, F:I.29, F:Y.61, F:I.91, F:F.113, F:L.115, G:L.49, G:L.49, G:A.53 Hydrogen bonds: F:Y.63, F:Y.63, F:Y.63, F:Q.89, G:Q.52 pi-Stacking: G:H.83 Halogen bonds: G:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.7: 17 residues within 4Å: Chain A: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 Chain G: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain G Hydrophobic interactions: A:L.49, A:L.49, A:A.53, G:L.24, G:D.27, G:I.29, G:Y.61, G:Y.61, G:Y.63, G:I.91, G:L.115 Hydrogen bonds: A:Q.52, G:Y.63, G:Y.63, G:Y.63, G:Q.89 Water bridges: A:H.83 Halogen bonds: A:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.8: 19 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain I: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 18 PLIP interactions: 12 interactions with chain H, 6 interactions with chain I Hydrophobic interactions: H:L.24, H:D.27, H:I.29, H:Y.61, H:Y.63, H:I.91, H:F.113, H:L.115, I:L.49, I:L.49, I:A.53 Hydrogen bonds: H:Y.63, H:Y.63, H:Y.63, H:Q.89, I:Q.52 Water bridges: I:H.83 Halogen bonds: I:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.9: 17 residues within 4Å: Chain I: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain J: V.45, L.49, A.53, D.79, T.80, H.83 19 PLIP interactions: 5 interactions with chain J, 14 interactions with chain I Hydrophobic interactions: J:L.49, J:L.49, J:A.53, I:L.24, I:D.27, I:I.29, I:Y.61, I:Y.61, I:Y.63, I:I.91, I:F.113, I:L.115 Hydrogen bonds: J:Q.52, I:Y.63, I:Y.63, I:Y.63, I:Q.89 Halogen bonds: J:D.79 Water bridges: I:D.59 OO1-WFP-SER-PRO-YCP-ALA-MP8.10: 16 residues within 4Å: Chain J: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain K: V.45, L.49, A.53, T.80, H.83 16 PLIP interactions: 12 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:L.24, J:D.27, J:I.29, J:Y.61, J:I.91, J:I.93, J:F.113, J:L.115, K:L.49, K:L.49, K:A.53 Hydrogen bonds: J:Y.63, J:Y.63, J:Y.63, J:Q.89, K:Q.52 OO1-WFP-SER-PRO-YCP-ALA-MP8.11: 18 residues within 4Å: Chain K: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain L: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 18 PLIP interactions: 13 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:L.24, K:D.27, K:I.29, K:Y.61, K:Y.61, K:Y.63, K:I.91, K:F.113, K:L.115, L:L.49, L:L.49, L:A.53 Hydrogen bonds: K:Y.63, K:Y.63, K:Y.63, K:Q.89, L:Q.52 Halogen bonds: L:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.12: 17 residues within 4Å: Chain L: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain M: V.45, L.49, A.53, D.79, T.80, H.83 19 PLIP interactions: 13 interactions with chain L, 6 interactions with chain M Hydrophobic interactions: L:L.24, L:D.27, L:I.29, L:Y.61, L:Y.61, L:Y.63, L:I.91, L:F.113, L:L.115, M:L.49, M:L.49, M:A.53 Hydrogen bonds: L:Y.63, L:Y.63, L:Y.63, L:Q.89, M:Q.52 Water bridges: M:H.83 Halogen bonds: M:D.79 OO1-WFP-SER-PRO-YCP-ALA-MP8.13: 16 residues within 4Å: Chain M: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 Chain N: V.45, L.49, A.53, T.80, H.83 16 PLIP interactions: 3 interactions with chain N, 13 interactions with chain M Hydrophobic interactions: N:L.49, N:A.53, M:L.24, M:D.27, M:I.29, M:Y.61, M:Y.61, M:Y.63, M:I.91, M:F.113, M:L.115 Hydrogen bonds: N:Q.52, M:Y.63, M:Y.63, M:Y.63, M:Q.89 OO1-WFP-SER-PRO-YCP-ALA-MP8.14: 16 residues within 4Å: Chain H: V.45, L.49, A.53, T.80, H.83 Chain N: L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 15 PLIP interactions: 12 interactions with chain N, 3 interactions with chain H Hydrophobic interactions: N:L.24, N:D.27, N:I.29, N:Y.61, N:Y.63, N:I.91, N:F.113, N:L.115, H:L.49, H:A.53 Hydrogen bonds: N:Y.63, N:Y.63, N:Y.63, N:Q.89, H:Q.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Griffith, E.C. et al., Ureadepsipeptides as ClpP Activators. Acs Infect Dis. (2019)

Release Date

2019-11-06

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
I

I
K

J
L

K
M

L
N

M
S

N
T

ATP-dependent Clp protease proteolytic subunit

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