SMTL ID : 8cj4.1

Crystal structure of ClpP from Staphylococcus epidermidis, tetradecamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-14-mer

Ligands

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

MPD.1: 10 residues within 4Å: Chain A: 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 A Hydrophobic interactions: A:V.71, A:F.102, A:L.150, A:T.169 Hydrogen bonds: A:H.123, A:H.123 MPD.2: 8 residues within 4Å: Chain B: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.154 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.71, B:F.102 Hydrogen bonds: B:H.123, B:H.123 MPD.3: 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.4: 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:I.122, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.5: 9 residues within 4Å: Chain E: 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 E Hydrophobic interactions: E:V.71, E:F.102, E:L.150 Hydrogen bonds: E:H.123, E:H.123 MPD.6: 8 residues within 4Å: Chain F: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:V.71, F:F.102, F:L.150 Hydrogen bonds: F:H.123, F:H.123 MPD.7: 9 residues within 4Å: Chain G: 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 G Hydrophobic interactions: G:V.71, G:F.102, G:L.150 Hydrogen bonds: G:H.123, G:H.123 MPD.8: 11 residues within 4Å: Chain H: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:V.71, H:F.102, H:P.125, H:L.154 Hydrogen bonds: H:H.123, H:H.123, H:H.123 MPD.9: 9 residues within 4Å: Chain I: 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 I Hydrophobic interactions: I:V.71, I:F.102, I:L.150 Hydrogen bonds: I:H.123, I:H.123 MPD.10: 9 residues within 4Å: Chain J: 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 J Hydrophobic interactions: J:V.71, J:I.122, J:L.150 Hydrogen bonds: J:S.101, J:H.123, J:H.123 MPD.11: 9 residues within 4Å: Chain K: 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 K Hydrophobic interactions: K:V.71, K:F.102, K:L.150 Hydrogen bonds: K:H.123, K:H.123 MPD.12: 9 residues within 4Å: Chain L: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 7 PLIP interactions: 7 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 Water bridges: L:T.169 MPD.13: 8 residues within 4Å: Chain M: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 4 PLIP interactions: 4 interactions with chain M Hydrophobic interactions: M:F.102, M:L.150 Hydrogen bonds: M:H.123, M:H.123 MPD.14: 8 residues within 4Å: Chain N: V.71, S.98, M.99, S.101, F.102, I.122, H.123, 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

Alves Franca, B. et al., Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds. Sci Rep (2024)

Release Date

2024-01-17

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
H

I
I

J
J

K
K

L
L

M
M

N
N

ATP-dependent Clp protease proteolytic subunit