SMTL ID : 6jjk.1

Crystal structure of the DegP dodecamer with a modulator

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-12-mer

Ligands

24 x CYS- TYR- TYR- LYS- ILE: CYS-TYR-TYR-LYS-ILE(Non-covalent)

CYS-TYR-TYR-LYS-ILE.1: 13 residues within 4Å: Chain A: H.97, L.182, I.197, N.198, R.199, G.200, N.201, A.202, T.218, A.219, I.220, L.221, A.222 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.182, A:I.197, A:A.202 Hydrogen bonds: A:R.199, A:R.199, A:G.200, A:T.218, A:I.220, A:I.220, A:A.222 CYS-TYR-TYR-LYS-ILE.2: 12 residues within 4Å: Chain B: H.97, L.182, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221, A.222 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.182, B:I.197, B:A.202 Hydrogen bonds: B:H.97, B:R.199, B:R.199, B:G.200, B:I.220, B:I.220, B:A.222 CYS-TYR-TYR-LYS-ILE.3: 12 residues within 4Å: Chain C: H.97, L.182, N.183, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.182, C:N.183, C:I.197, C:A.202, C:I.220 Hydrogen bonds: C:E.188, C:G.200, C:I.220, C:I.220 CYS-TYR-TYR-LYS-ILE.4: 11 residues within 4Å: Chain D: H.97, L.182, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.182, D:I.197, D:A.202, D:I.220 Hydrogen bonds: D:G.200, D:I.220, D:I.220 CYS-TYR-TYR-LYS-ILE.5: 12 residues within 4Å: Chain E: 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:A.202, E:I.220, E:L.221 Hydrogen bonds: E:G.200, E:I.220, E:I.220 CYS-TYR-TYR-LYS-ILE.6: 8 residues within 4Å: Chain F: H.97, I.197, N.198, R.199, G.200, A.202, T.218, I.220 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:I.197, F:R.199, F:A.202, F:I.220 Hydrogen bonds: F:G.200, F:T.218, F:I.220 CYS-TYR-TYR-LYS-ILE.7: 15 residues within 4Å: Chain A: E.256, L.257, G.258, I.259, M.260, G.261, T.262, E.263, S.283, F.313, L.316, R.317 Chain L: Y.436, L.437, L.438 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain L Hydrophobic interactions: A:I.259, A:E.263, A:F.313, A:F.313, A:L.316, A:R.317 Hydrogen bonds: A:L.257, A:G.258, A:I.259, A:G.261, A:G.261, A:T.262, A:T.262, A:E.263, A:S.283, L:Y.436, L:L.438 CYS-TYR-TYR-LYS-ILE.8: 14 residues within 4Å: Chain B: E.256, L.257, G.258, I.259, M.260, G.261, T.262, S.283, F.313, R.317, V.320 Chain D: I.391, L.437, L.438 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:I.259, B:F.313, B:F.313, B:V.320 Hydrogen bonds: B:L.257, B:G.258, B:I.259, B:I.259, B:G.261, B:G.261, D:L.438 CYS-TYR-TYR-LYS-ILE.9: 8 residues within 4Å: Chain C: L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:I.259, C:F.313, C:F.313 Hydrogen bonds: C:L.257, C:G.258, C:I.259, C:I.259, C:G.261, C:G.261, C:T.262 CYS-TYR-TYR-LYS-ILE.10: 10 residues within 4Å: Chain D: E.256, L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317, V.320 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.257, D:F.313, D:V.320 Hydrogen bonds: D:L.257, D:G.258, D:I.259, D:I.259, D:I.259, D:G.261, D:G.261, D:T.262 CYS-TYR-TYR-LYS-ILE.11: 16 residues within 4Å: Chain A: Y.436, L.437, L.438 Chain E: A.184, E.185, E.256, L.257, G.258, I.259, M.260, G.261, T.262, S.283, F.313, R.317, V.320 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:I.259, E:F.313, E:F.313, E:V.320 Hydrogen bonds: E:A.184, E:L.257, E:G.258, E:I.259, E:I.259, E:G.261, E:G.261, E:R.317, A:Y.436, A:L.438 pi-Cation interactions: E:R.317 CYS-TYR-TYR-LYS-ILE.12: 9 residues within 4Å: Chain F: E.256, L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:I.259, F:F.313, F:R.317 Hydrogen bonds: F:L.257, F:G.258, F:I.259, F:I.259, F:I.259, F:G.261, F:G.261, F:T.262 CYS-TYR-TYR-LYS-ILE.13: 13 residues within 4Å: Chain G: H.97, L.182, I.197, N.198, R.199, G.200, N.201, A.202, T.218, A.219, I.220, L.221, A.222 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:L.182, G:I.197, G:A.202 Hydrogen bonds: G:R.199, G:R.199, G:G.200, G:T.218, G:I.220, G:I.220, G:A.222 CYS-TYR-TYR-LYS-ILE.14: 12 residues within 4Å: Chain H: H.97, L.182, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221, A.222 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:L.182, H:I.197, H:A.202 Hydrogen bonds: H:H.97, H:R.199, H:R.199, H:G.200, H:I.220, H:I.220, H:A.222 CYS-TYR-TYR-LYS-ILE.15: 12 residues within 4Å: Chain I: H.97, L.182, N.183, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:L.182, I:N.183, I:I.197, I:A.202, I:I.220 Hydrogen bonds: I:G.200, I:I.220, I:I.220 CYS-TYR-TYR-LYS-ILE.16: 11 residues within 4Å: Chain J: H.97, L.182, I.197, N.198, R.199, G.200, A.202, T.218, A.219, I.220, L.221 7 PLIP interactions: 7 interactions with chain J Hydrophobic interactions: J:L.182, J:I.197, J:A.202, J:I.220 Hydrogen bonds: J:G.200, J:I.220, J:I.220 CYS-TYR-TYR-LYS-ILE.17: 12 residues within 4Å: Chain K: 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:A.202, K:I.220, K:L.221 Hydrogen bonds: K:G.200, K:I.220, K:I.220 CYS-TYR-TYR-LYS-ILE.18: 8 residues within 4Å: Chain L: H.97, I.197, N.198, R.199, G.200, A.202, T.218, I.220 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:I.197, L:R.199, L:A.202, L:I.220 Hydrogen bonds: L:G.200, L:T.218, L:I.220 CYS-TYR-TYR-LYS-ILE.19: 15 residues within 4Å: Chain F: Y.436, L.437, L.438 Chain G: E.256, L.257, G.258, I.259, M.260, G.261, T.262, E.263, S.283, F.313, L.316, R.317 14 PLIP interactions: 1 interactions with chain F, 13 interactions with chain G Hydrogen bonds: F:L.438, G:L.257, G:G.258, G:I.259, G:G.261, G:G.261, G:E.263, G:S.283 Hydrophobic interactions: G:I.259, G:E.263, G:F.313, G:F.313, G:L.316, G:R.317 CYS-TYR-TYR-LYS-ILE.20: 14 residues within 4Å: Chain H: E.256, L.257, G.258, I.259, M.260, G.261, T.262, S.283, F.313, R.317, V.320 Chain J: I.391, L.437, L.438 14 PLIP interactions: 12 interactions with chain H, 2 interactions with chain J Hydrophobic interactions: H:I.259, H:F.313, H:F.313, H:V.320 Hydrogen bonds: H:L.257, H:G.258, H:I.259, H:I.259, H:I.259, H:G.261, H:G.261, H:T.262, J:L.438, J:L.438 CYS-TYR-TYR-LYS-ILE.21: 8 residues within 4Å: Chain I: L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:I.259, I:F.313, I:F.313 Hydrogen bonds: I:L.257, I:G.258, I:I.259, I:I.259, I:G.261, I:G.261 CYS-TYR-TYR-LYS-ILE.22: 10 residues within 4Å: Chain J: E.256, L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317, V.320 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:L.257, J:F.313, J:V.320 Hydrogen bonds: J:L.257, J:G.258, J:I.259, J:I.259, J:G.261, J:G.261 CYS-TYR-TYR-LYS-ILE.23: 16 residues within 4Å: Chain G: Y.436, L.437, L.438 Chain K: A.184, E.185, E.256, L.257, G.258, I.259, M.260, G.261, T.262, S.283, F.313, R.317, V.320 14 PLIP interactions: 13 interactions with chain K, 1 interactions with chain G Hydrophobic interactions: K:I.259, K:F.313, K:F.313, K:V.320 Hydrogen bonds: K:L.257, K:G.258, K:I.259, K:I.259, K:G.261, K:G.261, K:T.262, K:R.317, G:L.438 pi-Cation interactions: K:R.317 CYS-TYR-TYR-LYS-ILE.24: 9 residues within 4Å: Chain L: E.256, L.257, G.258, I.259, M.260, G.261, T.262, F.313, R.317 9 PLIP interactions: 9 interactions with chain L Hydrophobic interactions: L:I.259, L:F.313, L:R.317 Hydrogen bonds: L:L.257, L:G.258, L:I.259, L:I.259, L:G.261, L:G.261

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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