MolNFT v1 · #81800 · protein
Structure of the stapled P53 peptide bound to MDM2
3V3B · E3 ubiquitin-protein ligase MDM2: “Structure of the stapled P53 peptide bound to MDM2”. X-ray diffraction, 2 ligands (0EH, CL), 3 pockets (best druggability 0.37). MolNFT v1 #81800 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3V3B
- Type
- protein
- Length
- 195 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Sah-P53-8 stapled-peptide
- EC
- 6.3.2.-
- UniProt
- Q00987
- Ligands
- 0EH, CL
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 87 | 44% helix, 18% strand | Q00987 |
| C | Sah-P53-8 stapled-peptide | protein | 9 | 56% helix, 0% strand | — |
| D | Sah-P53-8 stapled-peptide | protein | 12 | 50% helix, 0% strand | — |
Ligands and binding sites
- 0EH · (2R)-2-amino-2-methylnonanoic acid · ligand · 2 copies · chains B, C, A, D
- CL · Chloride ion · ion · 8 copies · chains A, B
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 | 57 | 0.37 | 0.79 | 10 | 0EH |
| 2 | 51 | 0.36 | 0.80 | 13 | 0EH |
| 3 | 79 | 0.30 | 0.72 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–D · 523 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 3V3B · Structure of the Stapled p53 Peptide Bound to Mdm2 · the same entry in another collection · chain D against D, TM-score 1.00
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 Q00987
- Elsewhere: RCSB PDB 3V3B · PDBe 3V3B · UniProt Q00987
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.