Research workbench
The crystal structure of P53 DNA binding domain and puma complex
Analyse The crystal structure of P53 DNA binding domain and puma complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DVD
- Type
- protein
- Length
- 811 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular tumor antigen P53; BCL-2-binding component 3, isoforms 1/2
- UniProt
- P04637, Q9BXH1
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cellular tumor antigen P53 | protein | 199 | 9% helix, 35% strand | P04637 |
| E | BCL-2-binding component 3, isoforms 1/2 | protein | 15 | 20% helix, 0% strand | Q9BXH1 |
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
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.71 | 0.76 | 96 | empty |
| 2 | 812 | 0.70 | 0.76 | 99 | empty |
| 3 | 87 | 0.48 | 0.82 | 20 | empty |
| 4 | 160 | 0.47 | 0.77 | 29 | empty |
| 5 | 129 | 0.41 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–C · 646 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 337 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 235 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7DVD · The crystal structure of p53 DNA binding domain and PUMA complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BXH1 · AlphaFold monomer V2.0 prediction for BCL-2-binding component 3, isoforms 1/2 (Q9BXH1) · a predicted model of the same protein · chain E against A, TM-score 0.27
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
- Every structure of UniProt Q9BXH1
- Elsewhere: RCSB PDB 7DVD · PDBe 7DVD · UniProt P04637 · UniProt Q9BXH1
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