Research workbench
Human P53 core domain mutant M133L-V203A-N239Y-G245S-N268D
Analyse Human P53 core domain mutant M133L-V203A-N239Y-G245S-N268D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J1Y
- Type
- protein
- Length
- 768 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53
- UniProt
- P04637
- Ligands
- ZN, CA
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellular tumor antigen P53 | protein | 192 | 8% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 193 | 8% helix, 35% strand | P04637 |
| C | Cellular tumor antigen P53 | protein | 191 | 9% helix, 35% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 192 | 9% helix, 35% strand | P04637 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.65 | 0.78 | 75 | empty |
| 2 | 339 | 0.58 | 0.76 | 50 | CA |
| 3 | 236 | 0.57 | 0.79 | 40 | CA |
| 4 | 284 | 0.55 | 0.76 | 46 | empty |
| 5 | 152 | 0.48 | 0.78 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–D · 613 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 423 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 247 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2J1Y · Human p53 core domain mutant M133L-V203A-N239Y-G245S-N268D · 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 P04637
- Elsewhere: RCSB PDB 2J1Y · PDBe 2J1Y · UniProt P04637
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