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Crystal structure of P53 core domain in complex with DNA
Analyse Crystal structure of P53 core domain in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HJE
- Type
- protein + DNA
- Length
- 842 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; DNA (5'- D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP…
- UniProt
- P04637
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cellular tumor antigen P53 | protein | 200 | 11% helix, 34% strand | P04637 |
| E | DNA (5'- D(*TP*CP*AP*CP*AP*AP*GP*TP*TP*AP*GP*AP*GP*AP*CP*AP*AP*GP*CP*CP*T)- 3') | dna | 21 | — | — |
| F | DNA (5'- D(*AP*GP*GP*CP*TP*TP*GP*TP*CP*TP*CP*TP*AP*AP*CP*TP*TP*GP*TP*GP*A)- 3') | dna | 21 | — | — |
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
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.68 | 0.85 | 26 | empty |
| 2 | 305 | 0.68 | 0.83 | 35 | empty |
| 3 | 319 | 0.68 | 0.82 | 36 | empty |
| 4 | 352 | 0.66 | 0.80 | 33 | empty |
| 5 | 370 | 0.55 | 0.74 | 34 | empty |
Interfaces
13 interfaces between chains.
- E–F · 900 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–D · 463 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 434 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 417 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4HJE · Crystal structure of p53 core domain in complex with DNA · 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 P04637
- Elsewhere: RCSB PDB 4HJE · PDBe 4HJE · UniProt P04637
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