Research workbench
X-ray structure of MDM2 with modified P53 peptide
Analyse X-ray structure of MDM2 with modified P53 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AD0
- Type
- protein
- Length
- 596 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Modified P53 peptide
- EC
- 2.3.2.27
- UniProt
- Q00987
- Ligands
- 9FB
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 90 | 41% helix, 16% strand | Q00987 |
| B, D, E, F | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 87 | 45% helix, 18% strand | Q00987 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 2.3.2.27) | protein | 86 | 45% helix, 19% strand | Q00987 |
| H, I, J, K, L, M | Modified P53 peptide | protein | 12 | 58% helix, 0% strand | — |
Ligands and binding sites
- 9FB · (1~{S},2~{R})-2-azanylcyclopentane-1-carboxylic acid · ligand · 6 copies · chains A, C, H, B, I, J, D, K, E, L, F, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.67 | 0.78 | 44 | empty |
| 2 | 122 | 0.66 | 0.88 | 21 | empty |
| 3 | 137 | 0.58 | 0.83 | 23 | empty |
| 4 | 112 | 0.43 | 0.77 | 19 | empty |
| 5 | 84 | 0.38 | 0.76 | 19 | empty |
Interfaces
16 interfaces between chains.
- A–C · 664 Ų buried · 11 hydrogen bonds · protein-protein
- D–K · 627 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 627 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 626 Ų buried · 4 hydrogen bonds · protein-protein
- E–L · 625 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 7AD0 · X-ray structure of Mdm2 with modified p53 peptide · the same entry in another collection · chain F against F, 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 7AD0 · PDBe 7AD0 · UniProt Q00987
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.