SMTL ID : 6cfd.1

ADEP4 bound to E. faecium ClpP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-14-mer

Ligands

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

MPD.1: 9 residues within 4Å: Chain A: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.125, A:L.154 Hydrogen bonds: A:S.98, A:S.101, A:H.123 MPD.3: 9 residues within 4Å: Chain B: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.125, B:L.154 Hydrogen bonds: B:S.98, B:H.123 Water bridges: B:M.99 MPD.4: 9 residues within 4Å: Chain C: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:P.125, C:L.154 Hydrogen bonds: C:S.98, C:H.123 Water bridges: C:L.126 MPD.6: 9 residues within 4Å: Chain D: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:P.125, D:L.154 Hydrogen bonds: D:S.98, D:H.123 Water bridges: D:L.126 MPD.8: 9 residues within 4Å: Chain E: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:P.125, E:L.154 Hydrogen bonds: E:S.98, E:H.123 MPD.10: 9 residues within 4Å: Chain F: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:P.125, F:L.154 Hydrogen bonds: F:S.98, F:H.123 Water bridges: F:M.99 MPD.12: 9 residues within 4Å: Chain G: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:P.125, G:L.154 Hydrogen bonds: G:S.98, G:H.123 Water bridges: G:M.99 MPD.13: 9 residues within 4Å: Chain H: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:P.125, H:L.154 Hydrogen bonds: H:S.101, H:H.123 MPD.15: 9 residues within 4Å: Chain I: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:P.125, I:L.154 Hydrogen bonds: I:S.98, I:H.123 Water bridges: I:L.126 MPD.16: 9 residues within 4Å: Chain J: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:P.125, J:L.154 Hydrogen bonds: J:S.98 Water bridges: J:M.99 MPD.18: 9 residues within 4Å: Chain K: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:P.125, K:L.154 Hydrogen bonds: K:S.98, K:H.123 Water bridges: K:M.99 MPD.20: 9 residues within 4Å: Chain L: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 6 PLIP interactions: 6 interactions with chain L Hydrophobic interactions: L:P.125, L:L.154 Hydrogen bonds: L:S.98, L:H.123 Water bridges: L:M.99, L:L.126 MPD.22: 9 residues within 4Å: Chain M: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:P.125, M:L.154 Hydrogen bonds: M:S.98, M:H.123 Water bridges: M:M.99 MPD.24: 9 residues within 4Å: Chain N: S.98, M.99, S.101, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain N Hydrophobic interactions: N:P.125, N:L.154 Hydrogen bonds: N:S.98, N:H.123 Water bridges: N:M.99

11 x EZA: N-[(6aS,12S,15aS,17R,21R,23aS)-17,21-dimethyl-6,11,15,20,23-pentaoxooctadecahydro-2H,6H,11H,15H-pyrido[2,1-i]dipyrrolo[2,1-c:2',1'-l][1,4,7,10,13]oxatetraazacyclohexadecin-12-yl]-3,5-difluoro-Nalpha-[(2E)-hept-2-enoyl]-L-phenylalaninamide(Non-covalent)

EZA.2: 13 residues within 4Å: Chain A: D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain B: L.49, F.50, D.79, T.80, F.83 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.49, B:L.49, B:F.50, B:F.83, A:D.27, A:Y.61, A:Y.61, A:L.115 pi-Stacking: B:F.83, A:Y.63 Halogen bonds: B:D.79 Hydrogen bonds: A:Y.63, A:Y.63 EZA.5: 13 residues within 4Å: Chain C: R.23, D.27, Y.61, Y.63, Q.89, I.91, M.93, L.115, M.190 Chain D: L.49, A.53, T.80, F.83 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:L.49, D:A.53, D:F.83, C:Y.61, C:L.115 pi-Stacking: D:F.83, C:Y.63 Hydrogen bonds: C:Y.63, C:Y.63 EZA.7: 14 residues within 4Å: Chain D: R.23, D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain E: L.49, F.50, A.53, T.80, F.83 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:F.50, E:A.53, E:F.83, D:I.29, D:Y.61, D:Y.61, D:L.115 pi-Stacking: E:F.83, D:Y.63 Hydrogen bonds: D:Y.63, D:Y.63 EZA.9: 14 residues within 4Å: Chain E: R.23, D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain F: L.49, F.50, A.53, T.80, F.83 11 PLIP interactions: 7 interactions with chain E, 4 interactions with chain F Hydrophobic interactions: E:I.29, E:Y.61, E:Y.61, E:L.115, F:F.50, F:A.53, F:F.83 Hydrogen bonds: E:Y.63, E:Y.63 pi-Stacking: E:Y.63, F:F.83 EZA.11: 13 residues within 4Å: Chain F: D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain G: L.49, F.50, A.53, T.80, F.83 11 PLIP interactions: 6 interactions with chain F, 5 interactions with chain G Hydrophobic interactions: F:Y.61, F:Y.61, F:L.115, G:L.49, G:F.50, G:A.53, G:F.83 Hydrogen bonds: F:Y.63, F:Y.63 pi-Stacking: F:Y.63, G:F.83 EZA.14: 15 residues within 4Å: Chain H: L.24, D.27, I.29, Y.61, Y.63, Q.89, M.93, F.113, L.115, M.190 Chain I: L.49, F.50, A.53, T.80, F.83 14 PLIP interactions: 4 interactions with chain I, 10 interactions with chain H Hydrophobic interactions: I:F.50, I:A.53, I:F.83, H:L.24, H:I.29, H:Y.61, H:Y.61, H:F.113, H:L.115 pi-Stacking: I:F.83, H:Y.63 Hydrogen bonds: H:Y.63, H:Y.63, H:Q.89 EZA.17: 14 residues within 4Å: Chain J: L.24, D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain K: L.49, F.50, A.53, T.80, F.83 11 PLIP interactions: 5 interactions with chain K, 6 interactions with chain J Hydrophobic interactions: K:L.49, K:F.50, K:A.53, K:F.83, J:L.24, J:Y.61, J:L.115 pi-Stacking: K:F.83, J:Y.63 Hydrogen bonds: J:Y.63, J:Y.63 EZA.19: 14 residues within 4Å: Chain K: R.23, D.27, I.29, Y.61, Y.63, Q.89, M.93, L.115, M.190 Chain L: L.49, F.50, A.53, T.80, F.83 11 PLIP interactions: 6 interactions with chain K, 5 interactions with chain L Hydrophobic interactions: K:Y.61, K:Y.61, K:L.115, L:L.49, L:F.50, L:A.53, L:F.83 Hydrogen bonds: K:Y.63, K:Y.63 pi-Stacking: K:Y.63, L:F.83 EZA.21: 15 residues within 4Å: Chain L: R.23, D.27, I.29, Y.61, Y.63, Q.89, M.93, F.113, L.115, M.190 Chain M: L.49, F.50, A.53, T.80, F.83 12 PLIP interactions: 5 interactions with chain M, 7 interactions with chain L Hydrophobic interactions: M:L.49, M:F.50, M:A.53, M:F.83, L:Y.61, L:Y.61, L:F.113, L:L.115 pi-Stacking: M:F.83, L:Y.63 Hydrogen bonds: L:Y.63, L:Y.63 EZA.23: 15 residues within 4Å: Chain M: R.23, D.27, I.29, Y.61, Y.63, Q.89, I.91, M.93, F.113, L.115, M.190 Chain N: L.49, A.53, T.80, F.83 12 PLIP interactions: 7 interactions with chain M, 5 interactions with chain N Hydrophobic interactions: M:Y.61, M:I.91, M:F.113, M:L.115, N:L.49, N:L.49, N:A.53, N:F.83 Hydrogen bonds: M:Y.63, M:Y.63 pi-Stacking: M:Y.63, N:F.83 EZA.25: 14 residues within 4Å: Chain H: L.49, A.53, T.80, F.83 Chain N: R.23, D.27, I.29, Y.61, Y.63, Q.89, M.93, F.113, L.115, M.190 11 PLIP interactions: 4 interactions with chain H, 7 interactions with chain N Hydrophobic interactions: H:L.49, H:A.53, H:F.83, N:Y.61, N:Y.61, N:F.113, N:L.115 pi-Stacking: H:F.83, N:Y.63 Hydrogen bonds: N:Y.63, N:Y.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown Gandt, A. et al., In VivoandIn VitroEffects of a ClpP-Activating Antibiotic against Vancomycin-Resistant Enterococci. Antimicrob. Agents Chemother. (2018)

Release Date

2018-05-16

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