SMTL ID : 6jjo.1

Crystal structure of the DegP dodecamer with a modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.16 Å

Oligo State

homo-12-mer

Ligands

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

CYS-TYR-ARG-LYS-LEU.1: 10 residues within 4Å: Chain A: H.126, L.211, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.211, A:A.231 Hydrogen bonds: A:H.126, A:G.229, A:I.249, A:I.249 CYS-TYR-ARG-LYS-LEU.2: 7 residues within 4Å: Chain A: E.285, I.288, M.289, G.290, T.291, F.342, R.346 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.288, A:F.342 Hydrogen bonds: A:I.288, A:G.290, A:G.290, A:T.291 CYS-TYR-ARG-LYS-LEU.3: 10 residues within 4Å: Chain B: H.126, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250, A.251 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.231 Hydrogen bonds: B:T.247, B:I.249, B:I.249 CYS-TYR-ARG-LYS-LEU.4: 7 residues within 4Å: Chain B: Y.216, I.288, M.289, G.290, T.291, F.342, R.346 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:M.289 Hydrogen bonds: B:Y.216, B:I.288, B:G.290, B:G.290, B:T.291 CYS-TYR-ARG-LYS-LEU.5: 9 residues within 4Å: Chain C: H.126, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:A.231 Hydrogen bonds: C:H.126, C:G.229, C:I.249, C:I.249 CYS-TYR-ARG-LYS-LEU.6: 7 residues within 4Å: Chain C: E.285, L.286, G.287, I.288, M.289, G.290, R.346 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.285 Hydrogen bonds: C:I.288 CYS-TYR-ARG-LYS-LEU.7: 9 residues within 4Å: Chain D: L.211, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.211, D:A.231 Hydrogen bonds: D:H.126, D:G.229, D:I.249, D:I.249 CYS-TYR-ARG-LYS-LEU.8: 6 residues within 4Å: Chain D: E.285, L.286, G.287, I.288, M.289, G.290 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.288 Hydrogen bonds: D:L.286, D:G.287, D:I.288, D:I.288, D:G.290, D:G.290 CYS-TYR-ARG-LYS-LEU.9: 11 residues within 4Å: Chain E: H.126, L.211, N.227, G.229, A.231, T.247, A.248, I.249, L.250, A.251, P.252 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.211, E:A.231 Hydrogen bonds: E:H.126, E:G.229, E:I.249, E:I.249, E:A.251 CYS-TYR-ARG-LYS-LEU.10: 9 residues within 4Å: Chain E: E.285, L.286, G.287, I.288, M.289, G.290, T.291, F.342, R.346 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.286, E:G.287, E:I.288, E:G.290, E:G.290 CYS-TYR-ARG-LYS-LEU.11: 6 residues within 4Å: Chain F: H.126, L.211, A.231, T.247, A.248, I.249 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.211, F:A.248 Hydrogen bonds: F:T.247 CYS-TYR-ARG-LYS-LEU.12: 7 residues within 4Å: Chain F: L.286, G.287, I.288, M.289, G.290, F.342, R.346 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.288, F:F.342 Hydrogen bonds: F:L.286, F:G.287, F:I.288, F:I.288, F:G.290, F:G.290 CYS-TYR-ARG-LYS-LEU.13: 10 residues within 4Å: Chain G: H.126, L.211, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:L.211, G:A.231 Hydrogen bonds: G:H.126, G:G.229, G:I.249, G:I.249 CYS-TYR-ARG-LYS-LEU.14: 7 residues within 4Å: Chain G: E.285, I.288, M.289, G.290, T.291, F.342, R.346 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:I.288, G:F.342 Hydrogen bonds: G:I.288, G:G.290, G:G.290 CYS-TYR-ARG-LYS-LEU.15: 10 residues within 4Å: Chain H: H.126, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250, A.251 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:A.231 Hydrogen bonds: H:T.247, H:I.249, H:I.249 CYS-TYR-ARG-LYS-LEU.16: 7 residues within 4Å: Chain H: Y.216, I.288, M.289, G.290, T.291, F.342, R.346 6 PLIP interactions: 6 interactions with chain H Hydrophobic interactions: H:M.289 Hydrogen bonds: H:I.288, H:G.290, H:G.290, H:T.291, H:T.291 CYS-TYR-ARG-LYS-LEU.17: 9 residues within 4Å: Chain I: H.126, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:A.231 Hydrogen bonds: I:H.126, I:G.229, I:I.249, I:I.249 CYS-TYR-ARG-LYS-LEU.18: 7 residues within 4Å: Chain I: E.285, L.286, G.287, I.288, M.289, G.290, R.346 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:E.285 Hydrogen bonds: I:I.288 CYS-TYR-ARG-LYS-LEU.19: 9 residues within 4Å: Chain J: L.211, N.227, R.228, G.229, A.231, T.247, A.248, I.249, L.250 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:L.211, J:A.231 Hydrogen bonds: J:H.126, J:G.229, J:I.249, J:I.249 CYS-TYR-ARG-LYS-LEU.20: 6 residues within 4Å: Chain J: E.285, L.286, G.287, I.288, M.289, G.290 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:I.288 Hydrogen bonds: J:L.286, J:G.287, J:I.288, J:I.288, J:G.290, J:G.290 CYS-TYR-ARG-LYS-LEU.21: 11 residues within 4Å: Chain K: H.126, L.211, N.227, G.229, A.231, T.247, A.248, I.249, L.250, A.251, P.252 8 PLIP interactions: 8 interactions with chain K Hydrophobic interactions: K:L.211, K:A.231 Hydrogen bonds: K:H.126, K:G.229, K:I.249, K:I.249, K:A.251, K:A.251 CYS-TYR-ARG-LYS-LEU.22: 9 residues within 4Å: Chain K: E.285, L.286, G.287, I.288, M.289, G.290, T.291, F.342, R.346 6 PLIP interactions: 6 interactions with chain K Hydrogen bonds: K:L.286, K:G.287, K:I.288, K:G.290, K:G.290, K:T.291 CYS-TYR-ARG-LYS-LEU.23: 6 residues within 4Å: Chain L: H.126, L.211, A.231, T.247, A.248, I.249 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:L.211, L:A.248 Hydrogen bonds: L:T.247 CYS-TYR-ARG-LYS-LEU.24: 7 residues within 4Å: Chain L: L.286, G.287, I.288, M.289, G.290, F.342, R.346 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:I.288, L:F.342 Hydrogen bonds: L:L.286, L:G.287, L:I.288, L:I.288, L:G.290, L:G.290

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