Research workbench
The 2.3A crystal structure of humanized xenopus MDM2 with RO5545353
Analyse The 2.3A crystal structure of humanized xenopus MDM2 with RO5545353 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LWV
- Type
- protein
- Length
- 255 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2
- EC
- 6.3.2.-
- UniProt
- P56273
- Ligands
- 20W, SO4
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 85 | 45% helix, 14% strand | P56273 |
Ligands and binding sites
- 20W · (2S,3R,4R,5R)-N-(4-carbamoyl-2-methoxyphenyl)-2'-chloro-4-(3-chloro-2-fluorophenyl)-2-(2,2-dimethylpropyl)-5'-oxo-4',5'-dihydrospiro[pyrrolidine-3,6'-thieno[3,2-b]pyrrole]-5-carboxamide · ligand · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.74 | 0.78 | 46 | 20W, SO4 |
| 2 | 94 | 0.43 | 0.78 | 17 | 20W |
Interfaces
2 interfaces between chains.
- A–B · 389 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 154 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4LWV · The 2.3A Crystal Structure of Humanized Xenopus MDM2 with RO5545353 · the same entry in another collection · chain A against A, TM-score 1.00
- P56273 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase MDM2 (P56273) · a predicted model of the same protein · chain A 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 P56273
- Elsewhere: RCSB PDB 4LWV · PDBe 4LWV · UniProt P56273
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.