SMTL ID : 8rx0.1

(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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(Covalent)

759.1: 8 residues within 4Å: Chain A: L.37, C.81, V.91 Chain B: P.46, I.56, H.57, S.58, Y.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.57, B:H.57, B:Y.59

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain H: C.33, H.68 No protein-ligand interaction detected (PLIP) ZN.3: 3 residues within 4Å: Chain H: C.63, H.65, D.85 No protein-ligand interaction detected (PLIP) ZN.4: 4 residues within 4Å: Chain H: C.41, C.44, C.56, H.70 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crowe, C. et al., Mechanism of degrader-targeted protein ubiquitinability. Sci Adv (2024)

Release Date

2024-03-06

Peptides

Isoform B of Bromodomain-containing protein 4: A
von Hippel-Lindau disease tumor suppressor: B
Elongin-C: C
Elongin-B: D
Cullin-2: E
Ubiquitin-conjugating enzyme E2 R1: F
NEDD8: G
E3 ubiquitin-protein ligase RBX1, N-terminally processed: H
Polyubiquitin-B: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

E
E

F
G

G
N

H
R

I
U

Isoform B of Bromodomain-containing protein 4

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

Cullin-2

Ubiquitin-conjugating enzyme E2 R1

NEDD8

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Polyubiquitin-B

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