SMTL ID : 8rx0.1

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

Coordinates

PDB Format

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: 27 residues within 4Å: Chain A: N.14, R.16, P.18, F.23, P.33, W.35, F.38, Y.45, P.46, R.54, I.56, H.57, S.58, Y.59, H.62, W.64 Chain I: W.26, P.27, V.32, A.36, L.37, G.38, L.39, Y.42, H.89, V.91, M.94 31 PLIP interactions: 11 interactions with chain I, 20 interactions with chain A Hydrophobic interactions: I:W.26, I:P.27, I:P.27, I:V.32, I:L.37, I:L.39, I:V.91, A:P.18, A:W.35, A:F.38, A:Y.45, A:Y.45, A:I.56, A:I.56, A:H.57, A:Y.59, A:H.62, A:W.64 Hydrogen bonds: I:Y.42, I:N.85, A:R.16, A:R.16, A:R.54, A:H.57, A:H.57, A:S.58, A:Y.59, A:Y.59, A:H.62 Water bridges: I:N.85, I:H.89

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain E: C.40, I.42, C.43, H.78, C.81 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.40, E:C.43, E:H.78, E:C.81 ZN.3: 4 residues within 4Å: Chain E: C.73, H.75, C.92, D.95 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.73, E:H.75, E:C.92, E:D.95, E:D.95 ZN.4: 5 residues within 4Å: Chain E: C.51, C.54, C.66, H.78, H.80 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.51, E:C.54, E:C.66, E:H.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crowe, C. et al., (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub. To Be Published

Release Date

2024-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
D

D
E

E
R

F
N

G
U

H
G

I
A

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Cullin-2

RBX1

NEDD8

Ubiquitin

Ubiquitin-conjugating enzyme E2 R1

Isoform B of Bromodomain-containing protein 4

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