SMTL ID : 6jjl.1

Crystal structure of the DegP dodecamer with a modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.20 Å

Oligo State

homo-12-mer

Ligands

24 x CYS- TYR- ARG- LYS- LEU: CYS-TYR-ARG-LYS-LEU(Non-covalent)

CYS-TYR-ARG-LYS-LEU.1: 11 residues within 4Å: Chain A: H.97, L.182, N.198, R.199, G.200, N.201, A.202, T.218, A.219, I.220, L.221 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.182 Hydrogen bonds: A:G.200, A:N.201, A:A.202, A:T.218, A:I.220, A:I.220 CYS-TYR-ARG-LYS-LEU.2: 8 residues within 4Å: Chain A: L.257, I.259, M.260, G.261, T.262, S.283, F.313 Chain L: L.438 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain L Hydrophobic interactions: A:I.259, A:F.313 Hydrogen bonds: A:L.257, A:I.259, A:G.261, A:T.262, A:S.283, L:L.438 CYS-TYR-ARG-LYS-LEU.3: 8 residues within 4Å: Chain B: H.97, L.182, N.198, A.202, T.218, A.219, I.220, L.221 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.182 Hydrogen bonds: B:I.220, B:I.220 CYS-TYR-ARG-LYS-LEU.4: 6 residues within 4Å: Chain B: I.259, M.260, G.261, T.262, F.313, R.317 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.259, B:G.261, B:G.261 CYS-TYR-ARG-LYS-LEU.5: 10 residues within 4Å: Chain C: H.97, L.182, I.197, N.198, R.199, A.202, T.218, A.219, I.220, L.221 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.197, C:A.202, C:I.220 Hydrogen bonds: C:T.218, C:I.220, C:I.220 CYS-TYR-ARG-LYS-LEU.6: 6 residues within 4Å: Chain C: L.257, I.259, M.260, G.261, T.262, F.313 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.259 Hydrogen bonds: C:L.257, C:I.259, C:G.261, C:G.261, C:T.262 CYS-TYR-ARG-LYS-LEU.7: 6 residues within 4Å: Chain D: N.198, R.199, A.202, T.218, I.220, A.222 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.218, D:I.220, D:I.220 CYS-TYR-ARG-LYS-LEU.8: 8 residues within 4Å: Chain D: L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.259, D:F.313, D:F.313 Hydrogen bonds: D:G.258, D:I.259, D:I.259, D:G.261, D:G.261 CYS-TYR-ARG-LYS-LEU.9: 13 residues within 4Å: Chain E: N.95, H.97, L.182, I.197, N.198, R.199, A.202, T.218, A.219, I.220, L.221, A.222, P.223 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.182, E:I.197, E:I.220, E:I.220 Hydrogen bonds: E:T.218, E:I.220, E:I.220, E:A.222 CYS-TYR-ARG-LYS-LEU.10: 5 residues within 4Å: Chain E: L.257, I.259, M.260, G.261, T.262 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.257, E:I.259, E:G.261, E:G.261, E:T.262 CYS-TYR-ARG-LYS-LEU.11: 5 residues within 4Å: Chain F: H.97, A.202, T.218, A.219, I.220 No protein-ligand interaction detected (PLIP) CYS-TYR-ARG-LYS-LEU.12: 7 residues within 4Å: Chain F: E.256, L.257, I.259, M.260, G.261, T.262, F.313 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.313 Hydrogen bonds: F:E.256, F:I.259, F:G.261, F:G.261, F:T.262 CYS-TYR-ARG-LYS-LEU.13: 11 residues within 4Å: Chain G: H.97, L.182, N.198, R.199, G.200, N.201, A.202, T.218, A.219, I.220, L.221 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:L.182 Hydrogen bonds: G:G.200, G:N.201, G:A.202, G:T.218, G:I.220, G:I.220 CYS-TYR-ARG-LYS-LEU.14: 8 residues within 4Å: Chain F: L.438 Chain G: L.257, I.259, M.260, G.261, T.262, S.283, F.313 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:I.259, G:F.313 Hydrogen bonds: G:L.257, G:I.259, G:G.261, F:L.438 CYS-TYR-ARG-LYS-LEU.15: 8 residues within 4Å: Chain H: H.97, L.182, N.198, A.202, T.218, A.219, I.220, L.221 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:L.182 Hydrogen bonds: H:I.220, H:I.220 CYS-TYR-ARG-LYS-LEU.16: 6 residues within 4Å: Chain H: I.259, M.260, G.261, T.262, F.313, R.317 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:I.259, H:G.261, H:G.261 CYS-TYR-ARG-LYS-LEU.17: 10 residues within 4Å: Chain I: H.97, L.182, I.197, N.198, R.199, A.202, T.218, A.219, I.220, L.221 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:I.197, I:A.202, I:I.220 Hydrogen bonds: I:T.218, I:I.220, I:I.220 CYS-TYR-ARG-LYS-LEU.18: 6 residues within 4Å: Chain I: L.257, I.259, M.260, G.261, T.262, F.313 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:I.259 Hydrogen bonds: I:L.257, I:I.259, I:G.261, I:G.261 CYS-TYR-ARG-LYS-LEU.19: 6 residues within 4Å: Chain J: N.198, R.199, A.202, T.218, I.220, A.222 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:T.218, J:I.220, J:I.220 CYS-TYR-ARG-LYS-LEU.20: 8 residues within 4Å: Chain J: L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:I.259, J:F.313, J:F.313 Hydrogen bonds: J:G.258, J:I.259, J:I.259, J:G.261, J:G.261, J:T.262 CYS-TYR-ARG-LYS-LEU.21: 13 residues within 4Å: Chain K: N.95, H.97, L.182, I.197, N.198, R.199, A.202, T.218, A.219, I.220, L.221, A.222, P.223 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:L.182, K:I.197, K:I.220, K:I.220 Hydrogen bonds: K:T.218, K:I.220, K:I.220, K:A.222 CYS-TYR-ARG-LYS-LEU.22: 5 residues within 4Å: Chain K: L.257, I.259, M.260, G.261, T.262 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:L.257, K:I.259, K:G.261, K:G.261, K:T.262 CYS-TYR-ARG-LYS-LEU.23: 5 residues within 4Å: Chain L: H.97, A.202, T.218, A.219, I.220 No protein-ligand interaction detected (PLIP) CYS-TYR-ARG-LYS-LEU.24: 7 residues within 4Å: Chain L: E.256, L.257, I.259, M.260, G.261, T.262, F.313 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:F.313 Hydrogen bonds: L:I.259, L:G.261, L:G.261, L:T.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, H. et al., Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy. Commun Biol (2020)

Release Date

2020-09-02

Peptides

Periplasmic serine endoprotease DegP: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

Periplasmic serine endoprotease DegP

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