MolNFT v1 · #77938 · protein
A ring E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-ring ligases
3RTR · Cullin-1: “A ring E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-ring…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.83). MolNFT v1 #77938 on GenesisL1: 3D…
- PDB
- 3RTR
- Type
- protein
- Length
- 1,716 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cullin-1; E3 ubiquitin-protein ligase RBX1
- EC
- 6.3.2.-
- UniProt
- Q13616, P62877
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cullin-1 | protein | 353 | 52% helix, 13% strand | Q13616 |
| B | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 86 | 16% helix, 33% strand | P62877 |
| C | Cullin-1 | protein | 317 | 54% helix, 9% strand | Q13616 |
| D | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 79 | 18% helix, 27% strand | P62877 |
| E | Cullin-1 | protein | 359 | 50% helix, 14% strand | Q13616 |
| F | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 81 | 19% helix, 30% strand | P62877 |
| G | Cullin-1 | protein | 360 | 53% helix, 13% strand | Q13616 |
| H | E3 ubiquitin-protein ligase RBX1 (EC 6.3.2.-) | protein | 81 | 7% helix, 30% strand | P62877 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains F, D, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.83 | 0.86 | 78 | empty |
| 2 | 1040 | 0.82 | 0.83 | 94 | empty |
| 3 | 694 | 0.80 | 0.84 | 83 | empty |
| 4 | 759 | 0.79 | 0.83 | 61 | empty |
| 5 | 1151 | 0.77 | 0.79 | 87 | empty |
Interfaces
16 interfaces between chains.
- G–H · 2089 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1979 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1977 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 1631 Ų buried · 39 hydrogen bonds · protein-protein
- F–H · 1204 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3RTR · A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural… · the same entry in another collection · chain H against H, TM-score 1.00
- Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain G against A, TM-score 0.95
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 Q13616
- Every structure of UniProt P62877
- Elsewhere: RCSB PDB 3RTR · PDBe 3RTR · UniProt Q13616 · UniProt P62877
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