SMTL ID : 8r5h.1

Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.38, C.41, H.76, C.79 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.38, B:C.41, B:H.76, B:C.79 ZN.2: 4 residues within 4Å: Chain B: C.71, H.73, C.90, D.93 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:H.73, B:C.90, B:D.93 ZN.3: 4 residues within 4Å: Chain B: C.49, C.52, C.64, H.78 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.49, B:C.52, B:C.64, B:H.78

1 x SY8: 5-azanylpentan-2-one(Covalent)

SY8.4: 5 residues within 4Å: Chain C: N.85, C.93, S.138 Chain D: G.75 Chain F: C.23 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.85, C:C.93

1 x 759: (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

759.5: 22 residues within 4Å: Chain F: W.29, P.30, F.31, V.35, L.40, G.41, L.42, N.88, H.92, E.93, V.94, M.97 Chain H: W.35, Y.45, P.46, R.54, I.56, H.57, S.58, Y.59, H.62, W.64 16 PLIP interactions: 12 interactions with chain H, 4 interactions with chain F Hydrophobic interactions: H:W.35, H:Y.45, H:Y.45, H:I.56, H:I.56, H:W.64, F:W.29, F:P.30, F:F.31, F:L.40 Hydrogen bonds: H:Y.45, H:R.54, H:H.57, H:S.58, H:Y.59, H:H.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol.Cell (2024)

Release Date

2024-02-21

Peptides

Cullin-2: A
E3 ubiquitin-protein ligase RBX1, N-terminally processed: B
Ubiquitin-conjugating enzyme E2 R2: C
Ubiquitin: D
Elongin-C: E
Bromodomain-containing protein 4: F
Elongin-B: G
von Hippel-Lindau disease tumor suppressor: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
R

C
C

D
U

E
D

F
F

G
G

H
H

Cullin-2

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Ubiquitin-conjugating enzyme E2 R2

Ubiquitin

Elongin-C

Bromodomain-containing protein 4

Elongin-B

von Hippel-Lindau disease tumor suppressor

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