Research workbench
Human P53 core domain with hot spot mutation R249S and second site suppressor mutation H168R in sequence-specific complex with DNA
Analyse Human P53 core domain with hot spot mutation R249S and second site suppressor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D0A
- Type
- protein + DNA
- Length
- 823 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)- 3'); Cellular tumor antigen…
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)- 3') | dna | 11 | — | — |
| F | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)- 3') | dna | 10 | — | — |
| G | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)- 3') | dna | 12 | — | — |
| H | DNA (5'-D(*DCP*DGP*DGP*DGP*DCP*DAP*DTP*DGP*DCP*DCP*DCP*DG)- 3') | dna | 10 | — | — |
| A | Cellular tumor antigen P53 | protein | 196 | 9% helix, 34% strand | P04637 |
| B | Cellular tumor antigen P53 | protein | 197 | 9% helix, 34% strand | P04637 |
| C | Cellular tumor antigen P53 | protein | 193 | 8% helix, 34% strand | P04637 |
| D | Cellular tumor antigen P53 | protein | 194 | 8% helix, 34% strand | P04637 |
Ligands and binding sites
- ZN · Zinc 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
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.76 | 0.80 | 70 | empty |
| 2 | 388 | 0.73 | 0.84 | 35 | empty |
| 3 | 172 | 0.45 | 0.75 | 19 | empty |
| 4 | 132 | 0.42 | 0.75 | 23 | empty |
| 5 | 79 | 0.40 | 0.78 | 19 | empty |
Interfaces
19 interfaces between chains.
- G–H · 488 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- E–F · 484 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- F–A · 354 Ų buried · 8 hydrogen bonds · protein-nucleic
- H–D · 348 Ų buried · 8 hydrogen bonds · protein-nucleic
- G–C · 346 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3D0A · Human p53 core domain with hot spot mutation R249S and second site suppressor mutation… · the same entry in another collection · chain E against E, 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 3D0A · PDBe 3D0A · UniProt P04637
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