MolNFT v1 · #188184 · protein
Structure of mouse double minute 2 homolog (MDM2) ring domain in complex with MA242
7TFG · E3 ubiquitin-protein ligase MDM2: “Structure of mouse double minute 2 homolog (MDM2) ring domain in complex with MA242”. X-ray diffraction, 2 ligands (I2S, ZN), 4 pockets (best druggability 0.58). MolNFT v1 #188184 on GenesisL1: 3D…
- PDB
- 7TFG
- Type
- protein
- Length
- 258 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 2.3.2.27
- UniProt
- Q7YRZ8
- Ligands
- I2S, ZN
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 63 | 21% helix, 22% strand | Q7YRZ8 |
| C, D | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 66 | 20% helix, 29% strand | Q7YRZ8 |
Ligands and binding sites
- I2S · (7Z)-7-{[(4-chlorophenyl)methyl]imino}-1-(4-methylbenzene-1-sulfonyl)-3,4,5,7-tetrahydropyrrolo[4, 3,2-de]quinolin-8(1H)-one · ligand · chains A, B, C
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.58 | 0.80 | 31 | empty |
| 2 | 151 | 0.46 | 0.76 | 19 | empty |
| 3 | 70 | 0.37 | 0.78 | 13 | empty |
| 4 | 55 | 0.33 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1381 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1300 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 328 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 91 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- Q7YRZ8 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (Q7YRZ8) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q7YRZ8
- Elsewhere: RCSB PDB 7TFG · PDBe 7TFG · UniProt Q7YRZ8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.