SMTL ID : 8hla.1

Heteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F76C) (Naph@(MIX|3:3))

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

12 x FL3: 1-naphthalen-2-ylethanone(Covalent)

FL3.1: 11 residues within 4Å: Chain B: F.42, C.76, S.77, K.80 Chain K: C.42, T.43, P.44 Chain L: P.184, W.208, W.209 Ligands: FL3.11 5 PLIP interactions: 3 interactions with chain B, 1 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: B:F.42, B:F.42, B:K.80, K:P.44, L:W.208 FL3.2: 9 residues within 4Å: Chain C: G.163, V.164, A.165, V.182, P.183, P.184 Chain D: D.41, C.42, E.141 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:A.165, C:P.183, D:E.141 FL3.3: 10 residues within 4Å: Chain C: T.43, S.77, K.80, W.81, W.84 Chain D: W.209 Chain F: F.42, C.76, S.77, K.80 9 PLIP interactions: 5 interactions with chain C, 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: C:T.43, C:K.80, C:W.84, C:W.84, F:F.42, F:K.80, D:W.209 pi-Stacking: C:W.81 Hydrogen bonds: F:S.77 FL3.4: 10 residues within 4Å: Chain A: F.42, C.76, S.77, K.80 Chain C: W.209 Chain D: T.43, S.77, K.80, W.81, W.84 7 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:F.42, A:K.80, A:K.80, C:W.209, D:T.43, D:K.80, D:W.84 FL3.5: 10 residues within 4Å: Chain C: D.41, C.42 Chain D: S.159, G.163, V.164, A.165, I.181, V.182, P.183, P.184 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:A.165 FL3.6: 8 residues within 4Å: Chain E: C.76, S.77, K.80 Chain G: P.184, W.209 Chain H: C.42, P.44 Ligands: FL3.8 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: E:K.80, E:K.80, G:P.184, G:P.184, G:W.209 FL3.7: 9 residues within 4Å: Chain G: C.42, E.141 Chain H: G.163, V.164, A.165, I.181, V.182, P.183, P.184 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:E.141, H:A.165, H:P.183 FL3.8: 8 residues within 4Å: Chain E: F.42, S.77 Chain F: W.208, W.209 Chain H: C.42, K.80, W.84 Ligands: FL3.6 8 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: F:W.208, F:W.209, E:F.42, E:F.42, E:F.42, E:F.42 pi-Stacking: F:W.209, H:W.84 FL3.9: 9 residues within 4Å: Chain I: C.76, S.77, K.80 Chain K: W.209 Chain L: T.43, S.77, K.80, W.81, W.84 8 PLIP interactions: 1 interactions with chain K, 6 interactions with chain L, 1 interactions with chain I Hydrophobic interactions: K:W.209, L:T.43, L:K.80, L:W.81, L:W.84, L:W.84, I:K.80 pi-Stacking: L:W.81 FL3.10: 10 residues within 4Å: Chain G: T.43, D.73, K.80, W.81, W.84 Chain H: W.209 Chain J: F.42, C.76, S.77, K.80 9 PLIP interactions: 4 interactions with chain G, 4 interactions with chain J, 1 interactions with chain H Hydrophobic interactions: G:K.80, G:W.81, G:W.84, J:F.42, J:K.80, J:K.80 pi-Stacking: G:W.81, H:W.209 Hydrogen bonds: J:S.77 FL3.11: 10 residues within 4Å: Chain A: W.208, W.209 Chain B: F.42, S.77 Chain K: C.42, K.80, W.81, E.83, W.84 Ligands: FL3.1 8 PLIP interactions: 3 interactions with chain B, 1 interactions with chain K, 4 interactions with chain A Hydrophobic interactions: B:F.42, B:F.42, K:W.81, A:W.208, A:W.208, A:W.209 Hydrogen bonds: B:S.77 pi-Stacking: A:W.209 FL3.12: 9 residues within 4Å: Chain K: G.163, V.164, A.165, V.182, P.183, P.184 Chain L: D.41, C.42, E.141 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain K Hydrophobic interactions: L:E.141, K:A.165, K:P.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himiyama, T. et al., Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins. Bioconjug.Chem. (2023)

Release Date

2023-03-22

Peptides

Peroxiredoxin: ABEFIJ
Peroxiredoxin: CDGHKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

I
I

J
J

C
C

D
D

G
G

H
H

K
K

L
L

Peroxiredoxin

Peroxiredoxin

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