SMTL ID : 6pmd.1

Structure of ClpP from Staphylococcus aureus in complex with Acyldepsipeptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-14-mer

Ligands

11 x SHV- WFP- SER- PRO- YCP- ALA- MP8: SHV-WFP-SER-PRO-YCP-ALA-MP8 Acyldepsipeptide(Non-covalent)

SHV-WFP-SER-PRO-YCP-ALA-MP8.1: 19 residues within 4Å: Chain A: 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 B: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.24, A:D.27, A:Y.61, A:Y.61, A:Y.63, A:I.91, A:F.113, B:L.49, B:L.49, B:A.53, B:T.80 Hydrogen bonds: A:Y.63, A:Y.63, A:Q.89, B:Q.52 Halogen bonds: B:D.79 SHV-WFP-SER-PRO-YCP-ALA-MP8.2: 19 residues within 4Å: Chain B: 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 C: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.24, B:D.27, B:Y.61, B:Y.61, B:Y.63, B:I.93, B:F.113, C:L.49, C:F.50, C:A.53 Hydrogen bonds: B:Y.63, B:Y.63, B:Q.89, C:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.3: 16 residues within 4Å: Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, M.190 Chain D: L.49, Q.52, A.53, T.80, H.83 15 PLIP interactions: 12 interactions with chain C, 3 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.93, C:F.113, D:L.49, D:A.53 Hydrogen bonds: C:Y.63, C:Y.63, C:Q.89 pi-Stacking: C:Y.61 Water bridges: D:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.4: 19 residues within 4Å: Chain D: 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 E: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 18 PLIP interactions: 12 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:L.24, D:D.27, D:I.29, D:Y.61, D:Y.61, D:Y.63, D:I.91, D:I.93, D:F.113, E:L.49, E:L.49, E:A.53, E:T.80 Hydrogen bonds: D:Y.63, D:Y.63, D:Q.89, E:Q.52 Halogen bonds: E:D.79 SHV-WFP-SER-PRO-YCP-ALA-MP8.5: 19 residues within 4Å: Chain E: 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 F: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 15 PLIP interactions: 10 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:L.24, E:Y.61, E:Y.61, E:Y.63, E:I.91, E:F.113, E:L.115, F:L.49, F:A.53, F:T.80 Hydrogen bonds: E:Y.63, E:Y.63, E:Q.89, F:Q.52 Halogen bonds: F:D.79 SHV-WFP-SER-PRO-YCP-ALA-MP8.6: 18 residues within 4Å: Chain F: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, M.190 Chain G: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain G Hydrophobic interactions: F:L.24, F:D.27, F:Y.61, F:Y.61, F:Y.63, F:I.91, F:F.113, G:L.49, G:F.50, G:T.80 Hydrogen bonds: F:Y.63, F:Y.63, F:Q.89, G:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.7: 17 residues within 4Å: Chain I: 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 J: L.49, Q.52, A.53, T.80, H.83 13 PLIP interactions: 10 interactions with chain I, 3 interactions with chain J Hydrophobic interactions: I:L.24, I:Y.61, I:Y.61, I:Y.63, I:I.91, I:I.93, I:F.113, J:L.49, J:A.53 Hydrogen bonds: I:Y.63, I:Y.63, I:Q.89, J:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.8: 18 residues within 4Å: Chain J: 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 K: V.45, L.49, Q.52, A.53, T.80, H.83 12 PLIP interactions: 8 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: J:L.24, J:Y.61, J:Y.61, J:Y.63, J:F.113, K:L.49, K:L.49, K:A.53 Hydrogen bonds: J:Y.63, J:Y.63, J:Q.89, K:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.9: 18 residues within 4Å: Chain K: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115 Chain L: V.45, L.49, F.50, Q.52, A.53, T.80, H.83 16 PLIP interactions: 12 interactions with chain K, 4 interactions with chain L Hydrophobic interactions: K:L.24, K:D.27, K:Y.61, K:Y.61, K:Y.63, K:I.91, K:I.93, K:F.113, K:L.115, L:L.49, L:F.50, L:A.53 Hydrogen bonds: K:Y.63, K:Y.63, K:Q.89, L:Q.52 SHV-WFP-SER-PRO-YCP-ALA-MP8.10: 19 residues within 4Å: Chain M: 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 N: V.45, L.49, Q.52, A.53, D.79, T.80, H.83 14 PLIP interactions: 8 interactions with chain M, 6 interactions with chain N Hydrophobic interactions: M:L.24, M:D.27, M:Y.61, M:Y.63, M:F.113, N:L.49, N:L.49, N:A.53, N:T.80 Hydrogen bonds: M:Y.63, M:Y.63, M:Q.89, N:Q.52 Halogen bonds: N:D.79 SHV-WFP-SER-PRO-YCP-ALA-MP8.11: 16 residues within 4Å: Chain H: V.45, L.49, Q.52, A.53, T.80, H.83 Chain N: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, M.190 12 PLIP interactions: 9 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.61, N:Y.63, H:L.49, H:A.53 Hydrogen bonds: N:Y.63, N:Y.63, N:Q.89, H:Q.52

14 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.12: 8 residues within 4Å: Chain A: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.71, A:F.102, A:L.150 Hydrogen bonds: A:H.123, A:H.123 MPD.13: 10 residues within 4Å: Chain B: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.71, B:F.102, B:L.150, B:L.154 Hydrogen bonds: B:H.123, B:H.123 MPD.14: 8 residues within 4Å: Chain C: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.71, C:F.102, C:L.150 Hydrogen bonds: C:H.123, C:H.123 MPD.15: 9 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.71, D:F.102, D:L.150, D:L.154 Hydrogen bonds: D:H.123, D:H.123 MPD.16: 10 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.71, E:F.102, E:L.150, E:T.169 Hydrogen bonds: E:H.123, E:H.123 MPD.17: 9 residues within 4Å: Chain F: V.71, S.98, S.101, F.102, I.122, H.123, L.150, L.154, T.169 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:V.71, F:F.102, F:L.150, F:L.154, F:T.169 Hydrogen bonds: F:H.123, F:H.123 MPD.18: 8 residues within 4Å: Chain G: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:V.71, G:F.102, G:L.150 Hydrogen bonds: G:H.123, G:H.123 MPD.19: 9 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:V.71, H:F.102, H:L.150, H:L.154 Hydrogen bonds: H:H.123, H:H.123 MPD.20: 10 residues within 4Å: Chain I: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:V.71, I:F.102, I:I.122, I:L.150, I:L.154, I:T.169 Hydrogen bonds: I:H.123, I:H.123 MPD.21: 10 residues within 4Å: Chain J: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:V.71, J:F.102, J:L.150 Hydrogen bonds: J:H.123, J:H.123 MPD.22: 10 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154, T.169 7 PLIP interactions: 7 interactions with chain K Hydrophobic interactions: K:V.71, K:F.102, K:L.150, K:L.154, K:T.169 Hydrogen bonds: K:H.123, K:H.123 MPD.23: 9 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:V.71, L:F.102, L:I.122, L:L.150, L:L.154 Hydrogen bonds: L:H.123, L:H.123 Water bridges: L:M.99 MPD.24: 9 residues within 4Å: Chain M: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:V.71, M:F.102, M:L.150 Hydrogen bonds: M:H.123, M:H.123 MPD.25: 10 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:V.71, N:F.102, N:L.150 Hydrogen bonds: N:H.123, N:H.123

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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