SMTL ID : 9fsw.1

ClpP from Staphylococcus epidermidis with glycerol in some of the catalytic sites.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 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, Q.124, L.150, L.154 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.71, A:I.122 Hydrogen bonds: A:H.123 MPD.4: 12 residues within 4Å: Chain B: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169 Ligands: GOL.2 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.102, B:I.122, B:L.154, B:T.169 MPD.5: 9 residues within 4Å: Chain C: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.102 Hydrogen bonds: C:H.123 MPD.7: 10 residues within 4Å: Chain D: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.71, D:F.102, D:L.150 Hydrogen bonds: D:H.123, D:H.123 MPD.9: 10 residues within 4Å: Chain E: V.71, S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:V.71, E:F.102, E:I.122, E:L.150 Hydrogen bonds: E:H.123, E:H.123 MPD.11: 9 residues within 4Å: Chain F: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.102, F:I.122, F:L.150 Hydrogen bonds: F:H.123, F:H.123 MPD.13: 9 residues within 4Å: Chain G: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.102, G:L.150 Hydrogen bonds: G:H.123, G:H.123 MPD.15: 9 residues within 4Å: Chain H: S.98, M.99, S.101, F.102, I.122, H.123, P.125, L.150, L.154 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.102, H:I.122, H:L.154 MPD.17: 9 residues within 4Å: Chain I: S.98, M.99, S.101, F.102, I.122, H.123, L.150, L.154 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:L.150 Hydrogen bonds: I:H.123, I:H.123 MPD.18: 11 residues within 4Å: Chain J: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154, T.169 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:F.102, J:L.154, J:T.169 Hydrogen bonds: J:S.101, J:H.123 MPD.19: 11 residues within 4Å: Chain K: V.71, S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154 6 PLIP interactions: 6 interactions with chain K Hydrophobic interactions: K:V.71, K:F.102, K:L.154 Hydrogen bonds: K:S.101, K:H.123, K:H.123 MPD.20: 7 residues within 4Å: Chain L: S.98, M.99, S.101, F.102, I.122, H.123, L.154 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:F.102 Hydrogen bonds: L:S.101, L:H.123, L:H.123 MPD.21: 10 residues within 4Å: Chain M: S.98, M.99, S.101, F.102, I.122, H.123, Q.124, P.125, L.150, L.154 5 PLIP interactions: 5 interactions with chain M Hydrophobic interactions: M:I.122, M:L.150, M:L.154 Hydrogen bonds: M:H.123 Water bridges: M:L.126 MPD.23: 10 residues within 4Å: Chain N: V.71, S.98, S.101, F.102, I.122, H.123, Q.124, L.150, L.154 Ligands: GOL.24 7 PLIP interactions: 7 interactions with chain N Hydrophobic interactions: N:V.71, N:F.102, N:L.150, N:L.154 Hydrogen bonds: N:S.101, N:H.123, N:H.123

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain B: G.68, G.69, V.71, S.98, M.99, H.123, Q.124, P.125, L.126 Ligands: MPD.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.69, B:M.99, B:H.123, B:L.126, B:L.126 GOL.3: 5 residues within 4Å: Chain A: K.145 Chain B: D.172, N.173, F.174, L.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.172, B:F.174 GOL.6: 8 residues within 4Å: Chain D: G.68, G.69, S.98, M.99, H.123, P.125, L.126 Ligands: MPD.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.69, D:S.98, D:S.98, D:M.99, D:L.126, D:L.126 GOL.8: 10 residues within 4Å: Chain E: G.68, G.69, V.71, S.98, M.99, H.123, Q.124, P.125, L.126 Ligands: MPD.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.69, E:S.98, E:S.98, E:M.99, E:L.126, E:L.126 GOL.10: 9 residues within 4Å: Chain F: G.68, G.69, V.71, S.98, M.99, H.123, Q.124, L.126 Ligands: MPD.11 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.69, F:S.98, F:S.98, F:M.99, F:L.126, F:L.126 Water bridges: F:V.71 GOL.12: 4 residues within 4Å: Chain G: Q.35, P.67, G.68, G.69 No protein-ligand interaction detected (PLIP) GOL.14: 4 residues within 4Å: Chain H: Q.35, P.67, G.69, S.98 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:G.69, H:S.98, H:S.98 GOL.16: 10 residues within 4Å: Chain I: G.68, G.69, V.71, S.98, M.99, H.123, Q.124, P.125, L.126 Ligands: MPD.17 6 PLIP interactions: 6 interactions with chain I Hydrogen bonds: I:G.69, I:S.98, I:S.98, I:M.99, I:L.126, I:L.126 GOL.22: 2 residues within 4Å: Chain N: G.128, I.143 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:G.128 GOL.24: 7 residues within 4Å: Chain N: G.68, G.69, S.98, M.99, H.123, L.126 Ligands: MPD.23 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:G.69, N:S.98, N:S.98, N:M.99, N:L.126, N:L.126

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

2025-07-02

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

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