SMTL ID : 8grf.1

Crystal structure of F-box protein in the ternary complex with adaptor protein Skp1(DL) and its substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

hetero-2-1-1-mer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: R.440 Chain B: H.257, H.293, R.420 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.420, B:R.420, A:R.440 EDO.2: 7 residues within 4Å: Chain A: T.25, L.26, K.27, N.129, L.130, D.133, F.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.26, A:K.27, A:N.129 EDO.3: 5 residues within 4Å: Chain A: L.134, S.138, G.200, Y.228, N.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.231 Water bridges: A:M.135 EDO.4: 7 residues within 4Å: Chain B: L.78, H.257, H.339, L.342, D.346, R.348, N.392 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.257, B:R.348 EDO.5: 8 residues within 4Å: Chain B: T.25, L.26, K.27, W.114, N.129, L.130, D.133, F.192 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.25, B:L.26, B:K.27, B:N.129 EDO.6: 7 residues within 4Å: Chain B: P.291, L.292, H.293, G.294, R.295, A.296, E.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.291, B:R.295 EDO.7: 6 residues within 4Å: Chain C: I.186, I.189, T.191, A.205, S.206, L.224 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.191, C:T.191, C:S.206, C:S.206 Water bridges: B:Q.180 EDO.8: 8 residues within 4Å: Chain C: R.340, I.341, F.342, Y.344, Q.351, D.352, L.353, E.356 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.340, C:F.342, C:Y.344, C:D.352, C:D.352 EDO.9: 1 residues within 4Å: Chain D: D.175 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:Y.33 Hydrogen bonds: D:D.175 EDO.10: 4 residues within 4Å: Chain C: Q.351, D.352, L.353, G.354 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.351, C:D.352, C:L.353, C:G.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishio, K. et al., Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress. Sci Adv (2023)

Release Date

2023-04-26

Peptides

Citrate synthase: AB
F-box protein UCC1: C
E3 ubiquitin ligase complex SCF subunit: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Citrate synthase

F-box protein UCC1

E3 ubiquitin ligase complex SCF subunit

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