SMTL ID : 7c89.1

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant modified with 2-bromoacetophenone(Ph@ApPrx*)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-10-mer

Ligands

10 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 12 residues within 4Å: Chain A: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Chain B: A.170, I.186, P.188, P.189 Ligands: FL0.8 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.43, B:A.170 Hydrogen bonds: A:T.47, A:V.49, A:S.50 Salt bridges: A:R.126 FLC.3: 11 residues within 4Å: Chain A: A.170, P.188, P.189 Chain B: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Ligands: FL0.20 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.47, B:V.49, B:S.50, B:S.50 Salt bridges: B:R.126, B:R.126 Hydrophobic interactions: A:A.170 FLC.5: 12 residues within 4Å: Chain C: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Chain D: A.170, I.186, P.188, P.189 Ligands: FL0.14 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:T.47, D:A.170 Hydrogen bonds: C:V.49, C:S.50, C:S.50 Salt bridges: C:R.126, C:R.126 FLC.7: 11 residues within 4Å: Chain C: A.170, P.188, P.189 Chain D: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Ligands: FL0.2 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.47 Hydrogen bonds: D:V.49, D:S.50, D:S.50 Salt bridges: D:R.126, D:R.126 FLC.9: 12 residues within 4Å: Chain E: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Chain F: A.170, I.186, P.188, P.189 Ligands: FL0.18 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:V.49, E:S.50 Salt bridges: E:R.126, E:R.126 Hydrophobic interactions: F:A.170 FLC.11: 12 residues within 4Å: Chain E: A.170, I.186, P.188, P.189 Chain F: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Ligands: FL0.16 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:A.170, F:P.43 Hydrogen bonds: F:V.49, F:S.50, F:S.50 Salt bridges: F:R.126 FLC.13: 12 residues within 4Å: Chain G: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Chain H: A.170, I.186, P.188, P.189 Ligands: FL0.6 7 PLIP interactions: 7 interactions with chain G Hydrophobic interactions: G:T.47 Hydrogen bonds: G:T.47, G:V.49, G:S.50, G:S.50 Salt bridges: G:R.126, G:R.126 FLC.15: 12 residues within 4Å: Chain G: A.170, I.186, P.188, P.189 Chain H: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Ligands: FL0.12 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:P.43 Hydrogen bonds: H:T.47, H:V.49, H:S.50 Salt bridges: H:R.126 FLC.17: 11 residues within 4Å: Chain I: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Chain J: A.170, P.188, P.189 Ligands: FL0.10 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:T.47 Hydrogen bonds: I:V.49, I:S.50, I:M.145 Salt bridges: I:R.126, I:R.126 FLC.19: 12 residues within 4Å: Chain I: A.170, I.186, P.188, P.189 Chain J: P.43, T.47, P.48, V.49, S.50, R.126, M.145 Ligands: FL0.4 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:T.47 Hydrogen bonds: J:V.49, J:S.50, J:M.145 Salt bridges: J:R.126, J:R.126

10 x FL0: 2-bromanyl-1-phenyl-ethanone(Covalent)

FL0.2: 8 residues within 4Å: Chain A: S.78, V.79, C.80 Chain D: A.44, D.45, T.47, H.123 Ligands: FLC.7 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:A.44, D:T.47 pi-Stacking: D:H.123 Hydrogen bonds: A:V.79, A:C.80 FL0.4: 8 residues within 4Å: Chain B: S.78, V.79, C.80 Chain J: A.44, F.46, T.47, H.123 Ligands: FLC.19 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain B Hydrophobic interactions: J:A.44, J:T.47 Hydrogen bonds: B:V.79, B:C.80 FL0.6: 7 residues within 4Å: Chain C: S.78, V.79, C.80 Chain G: A.44, T.47, H.123 Ligands: FLC.13 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:A.44, G:T.47 pi-Stacking: G:H.123 Hydrogen bonds: C:V.79, C:C.80 FL0.8: 8 residues within 4Å: Chain A: A.44, T.47, H.123 Chain B: P.189 Chain D: S.78, V.79, C.80 Ligands: FLC.1 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: A:A.44, A:T.47, B:P.189 pi-Stacking: A:H.123 Hydrogen bonds: D:C.80 Water bridges: D:V.79 FL0.10: 8 residues within 4Å: Chain E: S.78, V.79, C.80 Chain I: A.44, T.47, H.123 Chain J: P.189 Ligands: FLC.17 5 PLIP interactions: 2 interactions with chain I, 2 interactions with chain E, 1 interactions with chain J Hydrophobic interactions: I:A.44, I:T.47, J:P.189 Hydrogen bonds: E:V.79, E:C.80 FL0.12: 7 residues within 4Å: Chain F: S.78, V.79, C.80 Chain H: A.44, T.47, H.123 Ligands: FLC.15 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain H Hydrogen bonds: F:C.80 Water bridges: F:V.79 Hydrophobic interactions: H:A.44, H:T.47 FL0.14: 8 residues within 4Å: Chain C: A.44, T.47, H.123 Chain D: P.190 Chain G: S.78, V.79, C.80 Ligands: FLC.5 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:A.44, C:T.47 Hydrogen bonds: G:V.79, G:C.80 FL0.16: 8 residues within 4Å: Chain E: P.189 Chain F: A.44, T.47, H.123 Chain H: S.78, V.79, C.80 Ligands: FLC.11 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: F:A.44, F:T.47, E:P.189 pi-Stacking: F:H.123 Hydrogen bonds: H:V.79, H:C.80 FL0.18: 7 residues within 4Å: Chain E: A.44, T.47, H.123 Chain I: S.78, V.79, C.80 Ligands: FLC.9 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain I Hydrophobic interactions: E:A.44, E:T.47 pi-Stacking: E:H.123 Hydrogen bonds: I:C.80 Water bridges: I:V.79 FL0.20: 7 residues within 4Å: Chain B: A.44, T.47, H.123 Chain J: S.78, V.79, C.80 Ligands: FLC.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain J Hydrophobic interactions: B:A.44 pi-Stacking: B:H.123 Hydrogen bonds: J:V.79, J:C.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Himiyama, T. et al., Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification. Bioconjug.Chem. (2021)

Release Date

2020-12-30

Peptides

Peroxiredoxin: ABCDEFGHIJ

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

Peroxiredoxin

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