MolNFT v1 · #82126 · protein + DNA
Structure of P73 DNA binding domain tetramer modulates P73 transactivation
3VD2 · Tumor protein P73: “Structure of P73 DNA binding domain tetramer modulates P73 transactivation”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.76). MolNFT v1 #82126 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VD2
- Type
- protein + DNA
- Length
- 1,291 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein P73; DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3')
- UniProt
- O15350
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tumor protein P73 | protein | 203 | 10% helix, 32% strand | O15350 |
| B | Tumor protein P73 | protein | 200 | 8% helix, 30% strand | O15350 |
| D | Tumor protein P73 | protein | 199 | 7% helix, 28% strand | O15350 |
| I, J | Tumor protein P73 | protein | 202 | 11% helix, 29% strand | O15350 |
| E, F, G, H | DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3') | dna | 14 | — | — |
| L | DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3') | dna | 13 | — | — |
| K | DNA (5'-D(*AP*TP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*AP*T)-3') | dna | 13 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.76 | 0.79 | 111 | empty |
| 2 | 1122 | 0.75 | 0.78 | 93 | empty |
| 3 | 626 | 0.75 | 0.82 | 47 | empty |
| 4 | 678 | 0.69 | 0.77 | 64 | empty |
| 5 | 332 | 0.65 | 0.80 | 50 | empty |
Interfaces
26 interfaces between chains.
- D–J · 840 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 630 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- G–H · 627 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- L–K · 566 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- C–H · 333 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3VD2 · 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 3VD2 · PDBe 3VD2 · UniProt O15350
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