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
- 602 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.07
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- E3 ubiquitin-protein ligase Mdm2; Modified p53 peptide
- EC
- 2.3.2.27
- UniProt
- Q00987
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.07 · 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 | 13 | 54% helix, 0% strand | — |
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 | 118 | 0.69 | 0.91 | 21 | empty |
| 2 | 484 | 0.67 | 0.78 | 44 | empty |
| 3 | 141 | 0.60 | 0.84 | 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
- A–H · 632 Ų buried · 4 hydrogen bonds · protein-protein
- D–K · 631 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 626 Ų buried · 5 hydrogen bonds · protein-protein
- C–J · 626 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 7AD0 · X-ray structure of MDM2 with modified P53 peptide · the same entry in another collection · chain A against A, 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
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