MolNFT v1 · #100040 · protein
Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase
4MLP · Cryptochrome-2: “Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase”. X-ray diffraction, 1 ligand (2CX), 16 pockets (best druggability 0.81). MolNFT v1 #100040 on GenesisL1: 3D structure…
- PDB
- 4MLP
- Type
- protein
- Length
- 1,968 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome-2
- UniProt
- Q9R194
- Ligands
- 2CX
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | Cryptochrome-2 | protein | 492 | 50% helix, 7% strand | Q9R194 |
Ligands and binding sites
- 2CX · N-[(2S)-3-(9H-carbazol-9-yl)-2-hydroxypropyl]-N-(furan-2-ylmethyl)methanesulfonamide · ligand · 4 copies · chains C, A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.81 | 0.82 | 65 | empty |
| 2 | 869 | 0.80 | 0.82 | 59 | empty |
| 3 | 485 | 0.78 | 0.85 | 49 | 2CX |
| 4 | 568 | 0.77 | 0.84 | 53 | 2CX |
| 5 | 638 | 0.77 | 0.82 | 50 | 2CX |
Interfaces
3 interfaces between chains.
- A–B · 724 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 677 Ų buried · 9 hydrogen bonds · protein-protein
- C–A · 280 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4MLP · Mammalian cryptochrome in complex with a small molecule competitor of its ubiquitin ligase · the same entry in another collection · chain D against D, TM-score 1.00
- Q9R194 · AlphaFold monomer V2.0 prediction for cryptochrome-2 (Q9R194) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9R194
- Elsewhere: RCSB PDB 4MLP · PDBe 4MLP · UniProt Q9R194
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