MolNFT v1 · #13492 · protein
Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf ubiquitin ligase complex
1LDD · Anaphase promoting complex: “Structure of the CUL1-RBX1-SKP1-F BOXSKP2 scf ubiquitin ligase complex”. X-ray diffraction, 3 pockets (best druggability 0.84). MolNFT v1 #13492 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1LDD
- Type
- protein
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaphase promoting complex
- UniProt
- Q12440
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Anaphase promoting complex | protein | 74 | 61% helix, 11% strand | Q12440 |
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.84 | 0.88 | 61 | empty |
| 2 | 108 | 0.54 | 0.83 | 14 | empty |
| 3 | 104 | 0.53 | 0.83 | 14 | empty |
Interfaces
6 interfaces between chains.
- B–C · 424 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 103 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1LDD · Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q12440 · AlphaFold monomer V2.0 prediction for anaphase-promoting complex subunit 2 (Q12440) · a predicted model of the same protein · chain C against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q12440
- Elsewhere: RCSB PDB 1LDD · PDBe 1LDD · UniProt Q12440
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