Research workbench
Structure of P73 DNA binding domain tetramer modulates P73 transactivation
Analyse Structure of P73 DNA binding domain tetramer modulates P73 transactivation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VD1
- Type
- protein + DNA
- Length
- 1,699 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein P73; DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3')
- UniProt
- O15350
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, L | Tumor protein P73 | protein | 202 | 10% helix, 31% strand | O15350 |
| B, D, I, J | Tumor protein P73 | protein | 199 | 12% helix, 35% strand | O15350 |
| C | Tumor protein P73 | protein | 201 | 9% helix, 33% strand | O15350 |
| E, F, G, H, M, N, O, P | DNA (5'-D(*CP*GP*GP*GP*CP*AP*TP*GP*CP*CP*CP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1005 | 0.82 | 0.83 | 105 | empty |
| 2 | 904 | 0.78 | 0.81 | 76 | empty |
| 3 | 978 | 0.77 | 0.80 | 89 | empty |
| 4 | 449 | 0.76 | 0.85 | 49 | empty |
| 5 | 630 | 0.75 | 0.81 | 59 | empty |
Interfaces
40 interfaces between chains.
- B–I · 765 Ų buried · 5 hydrogen bonds · protein-protein
- J–K · 678 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 4 hydrogen bonds · protein-protein
- M–N · 581 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- E–F · 579 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Compared structures
- 3VD1 · structure of p73 DNA binding domain tetramer modulates p73 transactivation · 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 O15350
- Elsewhere: RCSB PDB 3VD1 · PDBe 3VD1 · UniProt O15350
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