SMTL ID : 6ttz.1

Structure of the ClpP:ADEP4-complex from Staphylococcus aureus (open state)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-14-mer

Ligands

14 x NWT: N-[(2S)-3-(3,5-difluorophenyl)-1-[[(3S,9S,13S,15R,19S,22S)-15,19-dimethyl-2,8,12,18,21-pentaoxo-11-oxa-1,7,17,20-tetrazatetracyclo[20.4.0.03,7.013,17]hexacosan-9-yl]amino]-1-oxopropan-2-yl]heptanamide(Non-covalent)

NWT.1: 17 residues within 4Å: Chain A: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 Chain G: V.45, L.49, Q.52, A.53, T.80, H.83 11 PLIP interactions: 3 interactions with chain G, 8 interactions with chain A Hydrophobic interactions: G:L.49, A:L.24, A:Y.61, A:Y.63, A:I.91, A:L.115 Hydrogen bonds: G:Q.52, A:Y.63, A:Y.63, A:Q.89 pi-Stacking: G:H.83 NWT.2: 17 residues within 4Å: Chain A: V.45, L.49, A.53, T.80, H.83 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 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.24, B:Y.61, B:Y.61, B:Y.63, B:I.91, B:F.113, B:F.113, B:L.115, A:L.49 Hydrogen bonds: B:Y.63, B:Y.63, A:Q.52 pi-Stacking: A:H.83 NWT.3: 16 residues within 4Å: Chain B: V.45, L.49, T.80, H.83 Chain C: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:L.49, B:L.49, B:T.80, C:L.24, C:Y.61, C:Y.63, C:I.91, C:F.113, C:L.115 Hydrogen bonds: B:Q.52, C:Y.63, C:Y.63, C:Q.89 NWT.4: 17 residues within 4Å: Chain C: V.45, L.49, Q.52, A.53, T.80, H.83 Chain D: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain D Hydrophobic interactions: C:L.49, C:L.49, C:A.53, C:T.80, D:L.24, D:Y.61, D:Y.63, D:I.93 Hydrogen bonds: C:Q.52, D:Y.63, D:Y.63, D:Q.89 NWT.5: 21 residues within 4Å: Chain D: V.45, L.49, F.50, Q.52, A.53, D.79, T.80, H.83 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, E.193 15 PLIP interactions: 9 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:L.24, E:Y.61, E:Y.63, E:I.91, E:F.113, E:L.115, D:L.49, D:L.49, D:F.50 Hydrogen bonds: E:Y.63, E:Y.63, E:Q.89, D:Q.52 pi-Stacking: D:H.83 Halogen bonds: D:D.79 NWT.6: 18 residues within 4Å: Chain E: V.45, L.49, A.53, T.80, H.83 Chain F: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190, E.193 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.24, F:Y.61, F:Y.63, F:I.91, F:I.93, F:F.113, E:L.49 Hydrogen bonds: F:Y.63, F:Y.63, F:Q.89, E:Q.52 pi-Stacking: E:H.83 NWT.7: 16 residues within 4Å: Chain F: V.45, L.49, Q.52, A.53, T.80, H.83 Chain G: R.23, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 12 PLIP interactions: 5 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:L.49, F:L.49, F:L.49, G:Y.61, G:Y.63, G:I.91, G:L.115 Hydrogen bonds: F:Q.52, G:Y.63, G:Y.63, G:Q.89 pi-Stacking: F:H.83 NWT.8: 17 residues within 4Å: Chain H: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 Chain N: V.45, L.49, Q.52, A.53, T.80, H.83 11 PLIP interactions: 3 interactions with chain N, 8 interactions with chain H Hydrophobic interactions: N:L.49, H:L.24, H:Y.61, H:Y.63, H:I.91, H:L.115 Hydrogen bonds: N:Q.52, H:Y.63, H:Y.63, H:Q.89 pi-Stacking: N:H.83 NWT.9: 17 residues within 4Å: Chain H: V.45, L.49, A.53, T.80, H.83 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 13 PLIP interactions: 3 interactions with chain H, 10 interactions with chain I Hydrophobic interactions: H:L.49, I:L.24, I:Y.61, I:Y.61, I:Y.63, I:I.91, I:F.113, I:F.113, I:L.115 Hydrogen bonds: H:Q.52, I:Y.63, I:Y.63 pi-Stacking: H:H.83 NWT.10: 16 residues within 4Å: Chain I: V.45, L.49, T.80, H.83 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 13 PLIP interactions: 4 interactions with chain I, 9 interactions with chain J Hydrophobic interactions: I:L.49, I:L.49, I:T.80, J:L.24, J:Y.61, J:Y.63, J:I.91, J:F.113, J:L.115 Hydrogen bonds: I:Q.52, J:Y.63, J:Y.63, J:Q.89 NWT.11: 17 residues within 4Å: Chain J: V.45, L.49, Q.52, A.53, T.80, H.83 Chain K: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 12 PLIP interactions: 5 interactions with chain J, 7 interactions with chain K Hydrophobic interactions: J:L.49, J:L.49, J:A.53, J:T.80, K:L.24, K:Y.61, K:Y.63, K:I.93 Hydrogen bonds: J:Q.52, K:Y.63, K:Y.63, K:Q.89 NWT.12: 21 residues within 4Å: Chain K: V.45, L.49, F.50, Q.52, A.53, D.79, T.80, H.83 Chain L: R.23, L.24, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, F.113, L.115, M.190, E.193 15 PLIP interactions: 6 interactions with chain K, 9 interactions with chain L Hydrophobic interactions: K:L.49, K:L.49, K:F.50, L:L.24, L:Y.61, L:Y.63, L:I.91, L:F.113, L:L.115 Hydrogen bonds: K:Q.52, L:Y.63, L:Y.63, L:Q.89 pi-Stacking: K:H.83 Halogen bonds: K:D.79 NWT.13: 18 residues within 4Å: Chain L: V.45, L.49, A.53, T.80, H.83 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, E.193 12 PLIP interactions: 3 interactions with chain L, 9 interactions with chain M Hydrophobic interactions: L:L.49, M:L.24, M:Y.61, M:Y.63, M:I.91, M:I.93, M:F.113 Hydrogen bonds: L:Q.52, M:Y.63, M:Y.63, M:Q.89 pi-Stacking: L:H.83 NWT.14: 16 residues within 4Å: Chain M: V.45, L.49, Q.52, A.53, T.80, H.83 Chain N: R.23, D.27, I.29, Y.61, Y.63, Q.89, I.91, I.93, L.115, M.190 12 PLIP interactions: 7 interactions with chain N, 5 interactions with chain M Hydrophobic interactions: N:Y.61, N:Y.63, N:I.91, N:L.115, M:L.49, M:L.49, M:L.49 Hydrogen bonds: N:Y.63, N:Y.63, N:Q.89, M:Q.52 pi-Stacking: M:H.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malik, I.T. et al., Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. Chembiochem (2020)

Release Date

2020-03-25

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
A

I
B

J
C

K
D

L
E

M
F

N
G

ATP-dependent Clp protease proteolytic subunit

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