MolNFT v1 · #82124 · protein + DNA
Structure of P73 DNA binding domain tetramer modulates P73 transactivation
3VD0 · Tumor protein P73: “Structure of P73 DNA binding domain tetramer modulates P73 transactivation”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #82124 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3VD0
- Type
- protein + DNA
- Length
- 1,702 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein P73; DNA (5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3')
- UniProt
- O15350
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 9% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tumor protein P73 | protein | 202 | 7% helix, 33% strand | O15350 |
| B, L | Tumor protein P73 | protein | 201 | 8% helix, 31% strand | O15350 |
| D | Tumor protein P73 | protein | 200 | 10% helix, 35% strand | O15350 |
| I, J | Tumor protein P73 | protein | 199 | 10% helix, 33% strand | O15350 |
| K | Tumor protein P73 | protein | 206 | 11% helix, 30% strand | O15350 |
| E, H | DNA (5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3') | dna | 11 | — | — |
| F, G | DNA (5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3') | dna | 11 | — | — |
| M, N, O, P | DNA (5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*CP*TP*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 | 634 | 0.81 | 0.86 | 80 | empty |
| 2 | 756 | 0.80 | 0.84 | 94 | empty |
| 3 | 742 | 0.79 | 0.83 | 73 | empty |
| 4 | 342 | 0.77 | 0.87 | 42 | empty |
| 5 | 424 | 0.76 | 0.86 | 39 | empty |
Interfaces
43 interfaces between chains.
- B–I · 874 Ų buried · 5 hydrogen bonds · protein-protein
- J–K · 650 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 577 Ų buried · 8 hydrogen bonds · protein-protein
- O–P · 566 Ų buried · 60 hydrogen bonds · nucleic-nucleic
Compared structures
- 3VD0 · 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 3VD0 · PDBe 3VD0 · UniProt O15350
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