SMTL ID : 6ttu.1

Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2

Coordinates

PDB Format Compare

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 E: C.42, C.45, H.80, C.83 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.42, E:C.45, E:H.80, E:C.83 ZN.2: 4 residues within 4Å: Chain E: C.75, H.77, C.94, D.97 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.75, E:H.77, E:C.94, E:D.97, E:D.97 ZN.3: 4 residues within 4Å: Chain E: C.53, C.56, C.68, H.82 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.53, E:C.56, E:C.68, E:H.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baek, K. et al., NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly. Nature (2020)

Release Date

2020-02-12

Peptides

F-box/WD repeat-containing protein 1A: A
S-phase kinase-associated protein 1: B
Cullin-1: C
NEDD8: D
E3 ubiquitin-protein ligase RBX1: E
Ubiquitin-conjugating enzyme E2 D2: F
Polyubiquitin-C: G
CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
S

C
C

D
N

E
R

F
D

G
U

H
I

F-box/WD repeat-containing protein 1A

S-phase kinase-associated protein 1

Cullin-1

NEDD8

E3 ubiquitin-protein ligase RBX1

Ubiquitin-conjugating enzyme E2 D2

Polyubiquitin-C

CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY

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