MolNFT v1 · #81478 · protein + DNA
Structure of P63 DNA binding domain in complex with a 22 base pair response element containing a two base pair "gc" spacer between half sites
3US1 · Tumor protein 63: “Structure of P63 DNA binding domain in complex with a 22 base pair response element containing a two base…”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.35). MolNFT v1 #81478 on GenesisL1: 3D…
- PDB
- 3US1
- Type
- protein + DNA
- Length
- 397 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor protein 63; 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*GP*CP*AP*AP*AP*CP*AP*TP…
- UniProt
- Q9H3D4
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor protein 63 | protein | 193 | 5% helix, 36% strand | Q9H3D4 |
| D | Tumor protein 63 | protein | 182 | 12% helix, 38% strand | Q9H3D4 |
| F | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*GP*CP*AP*AP*AP*CP*AP*TP *GP*TP*TP*T)-3' | dna | 22 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.35 | 0.75 | 16 | empty |
| 2 | 73 | 0.28 | 0.73 | 15 | empty |
| 3 | 59 | 0.27 | 0.73 | 16 | empty |
| 4 | 50 | 0.25 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- D–F · 156 Ų buried · 1 hydrogen bond · protein-nucleic
- A–D · 112 Ų buried · 1 hydrogen bond · protein-protein
- A–F · 103 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3US1 · Structure of p63 DNA Binding Domain in Complex with a 22 Base Pair Response Element… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H3D4 · AlphaFold monomer V2.0 prediction for tumor protein 63 (Q9H3D4) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q9H3D4
- Elsewhere: RCSB PDB 3US1 · PDBe 3US1 · UniProt Q9H3D4
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