SMTL ID : 6n80.1

S. aureus ClpP bound to anti-4a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-14-mer

Ligands

14 x JT7: N-[(1R)-1-borono-3-methylbutyl]-N~2~-(2-chloro-4-methoxybenzene-1-carbonyl)-L-leucinamide(Covalent)

JT7.1: 15 residues within 4Å: Chain A: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.71, A:I.143, A:L.150 Hydrogen bonds: A:G.69, A:G.69, A:G.69, A:V.71, A:M.99, A:L.126, A:L.126 JT7.2: 14 residues within 4Å: Chain B: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.71, B:I.143 Hydrogen bonds: B:G.69, B:G.69, B:G.69, B:V.71, B:M.99, B:L.126, B:L.126, B:H.142 JT7.3: 14 residues within 4Å: Chain C: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.71, C:I.143 Hydrogen bonds: C:G.69, C:G.69, C:G.69, C:V.71, C:M.99, C:L.126, C:L.126, C:H.142 JT7.4: 15 residues within 4Å: Chain D: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:V.71, D:I.143, D:L.150 Hydrogen bonds: D:G.69, D:G.69, D:G.69, D:V.71, D:M.99, D:L.126, D:L.126 JT7.5: 15 residues within 4Å: Chain E: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:V.71, E:L.150 Hydrogen bonds: E:G.69, E:G.69, E:G.69, E:V.71, E:M.99, E:L.126, E:L.126, E:H.142 Water bridges: E:T.72 JT7.6: 16 residues within 4Å: Chain F: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, G.128, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:V.71, F:I.143, F:L.150 Hydrogen bonds: F:G.69, F:G.69, F:G.69, F:V.71, F:M.99, F:L.126, F:L.126 JT7.7: 15 residues within 4Å: Chain G: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:V.71, G:I.143, G:L.150 Hydrogen bonds: G:G.69, G:G.69, G:G.69, G:V.71, G:M.99, G:L.126, G:L.126 JT7.8: 15 residues within 4Å: Chain H: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:V.71, H:I.143, H:L.150 Hydrogen bonds: H:G.69, H:G.69, H:G.69, H:V.71, H:M.99, H:L.126, H:L.126 JT7.9: 15 residues within 4Å: Chain I: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:V.71, I:I.143, I:L.150 Hydrogen bonds: I:G.69, I:G.69, I:G.69, I:V.71, I:M.99, I:L.126, I:L.126 JT7.10: 15 residues within 4Å: Chain J: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:V.71, J:I.143, J:L.150 Hydrogen bonds: J:G.69, J:G.69, J:G.69, J:V.71, J:M.99, J:L.126, J:L.126 Water bridges: J:T.72 JT7.11: 15 residues within 4Å: Chain K: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:V.71, K:L.150 Hydrogen bonds: K:G.69, K:G.69, K:G.69, K:V.71, K:M.99, K:L.126, K:L.126 JT7.12: 16 residues within 4Å: Chain L: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, G.128, A.139, H.142, I.143, L.150 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:V.71, L:I.143, L:L.150 Hydrogen bonds: L:G.69, L:G.69, L:G.69, L:V.71, L:M.99, L:L.126, L:L.126 JT7.13: 15 residues within 4Å: Chain M: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 11 PLIP interactions: 11 interactions with chain M Hydrophobic interactions: M:V.71, M:I.143, M:L.150 Hydrogen bonds: M:G.69, M:G.69, M:G.69, M:V.71, M:M.99, M:L.126, M:L.126, M:H.142 JT7.14: 15 residues within 4Å: Chain N: G.68, G.69, S.70, V.71, S.98, M.99, H.123, Q.124, P.125, L.126, G.127, A.139, H.142, I.143, L.150 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:V.71, N:I.143, N:L.150 Hydrogen bonds: N:G.69, N:G.69, N:G.69, N:V.71, N:M.99, N:L.126, N:L.126, N:H.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, J. et al., De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX. J.Med.Chem. (2019)

Release Date

2019-06-26

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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