Research workbench
Structure of mouse double minute 2 homolog (MDM2) ring domain in complex with inulanolide a
Analyse Structure of mouse double minute 2 homolog (MDM2) ring domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7THL
- Type
- protein
- Length
- 261 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
- I61, ZN, CL
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 62 | 21% helix, 23% strand | Q7YRZ8 |
| B | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 66 | 20% helix, 26% strand | Q7YRZ8 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 65 | 18% helix, 22% strand | Q7YRZ8 |
| D | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 68 | 19% helix, 28% strand | Q7YRZ8 |
Ligands and binding sites
- I61 · Inulanolide A · ligand · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.40 | 0.74 | 22 | empty |
| 2 | 69 | 0.36 | 0.77 | 15 | empty |
| 3 | 59 | 0.33 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1370 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1235 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 293 Ų buried · 8 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 0.91
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 7THL · PDBe 7THL · UniProt Q7YRZ8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.