Research workbench
Crystal structure of an MDM2/P53 peptide complex
Analyse Crystal structure of an MDM2/P53 peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HFZ
- Type
- protein
- Length
- 197 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase MDM2; Cellular tumor antigen P53
- EC
- 6.3.2.-
- UniProt
- Q00987, P04637
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 83 | 46% helix, 13% strand | Q00987 |
| B, D | Cellular tumor antigen P53 | protein | 11 | 45% helix, 0% strand | P04637 |
| C | E3 ubiquitin-protein ligase MDM2 (EC 6.3.2.-) | protein | 92 | 45% helix, 14% strand | Q00987 |
Ligands and binding sites
- 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 | 228 | 0.47 | 0.74 | 48 | empty |
Interfaces
4 interfaces between chains.
- A–B · 587 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 561 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 136 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4HFZ · Crystal Structure of an MDM2/P53 Peptide Complex · 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
- Every structure of UniProt P04637
- Elsewhere: RCSB PDB 4HFZ · PDBe 4HFZ · UniProt Q00987 · UniProt P04637
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