MolNFT v1 · #95873 · protein
The 1.9A crystal structure of humanized xenopus MDM2 with nutlin-3A
4J3E · E3 ubiquitin-protein ligase MDM2: “The 1.9A crystal structure of humanized xenopus MDM2 with nutlin-3A”. X-ray diffraction, 2 ligands (NUT, SO4), 1 pocket (best druggability 0.40). MolNFT v1 #95873 on GenesisL1: 3D structure…
- PDB
- 4J3E
- Type
- protein
- Length
- 86 residues
- Chains
- 1
- 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
- NUT, SO4
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 86 | 44% helix, 13% strand | P56273 |
Ligands and binding sites
- NUT · 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.40 | 0.77 | 17 | NUT |
Compared structures
- 4J3E · The 1.9A crystal structure of humanized Xenopus Mdm2 with nutlin-3a · 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 0.96
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 4J3E · PDBe 4J3E · UniProt P56273
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