MolNFT v1 · #81479 · protein + DNA
Structure of P63 DNA binding domain in complex with a 19 base pair A/T rich response element containing two half sites with a single base pair overlap
3US2 · Tumor protein 63: “Structure of P63 DNA binding domain in complex with a 19 base pair A/T rich response element containing two…”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #81479 on GenesisL1…
- PDB
- 3US2
- Type
- protein + DNA
- Length
- 1,576 residues
- Chains
- 12
- 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*AP*AP*AP*CP*AP*TP*GP*TP*TP *T)-3'…
- UniProt
- Q9H3D4
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, I | Tumor protein 63 | protein | 193 | 5% helix, 37% strand | Q9H3D4 |
| B, D, H, J | Tumor protein 63 | protein | 182 | 12% helix, 38% strand | Q9H3D4 |
| E, K | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*AP*AP*AP*CP*AP*TP*GP*TP*TP *T)-3' | dna | 19 | — | — |
| F, L | 5'-D(*AP*AP*AP*CP*AP*TP*GP*TP*TP*TP*AP*AP*CP*AP*TP*GP*TP*TP *T)-3' | dna | 19 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, G, H, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.86 | 0.87 | 109 | empty |
| 2 | 488 | 0.81 | 0.88 | 70 | empty |
| 3 | 377 | 0.80 | 0.90 | 30 | empty |
| 4 | 401 | 0.80 | 0.89 | 27 | empty |
| 5 | 385 | 0.79 | 0.89 | 27 | empty |
Interfaces
32 interfaces between chains.
- K–L · 858 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- E–F · 857 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- H–I · 670 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 669 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 356 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3US2 · Structure of p63 DNA Binding Domain in Complex with a 19 Base Pair A/T Rich Response… · the same entry in another collection · chain L against L, 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 Q9H3D4
- Elsewhere: RCSB PDB 3US2 · PDBe 3US2 · UniProt Q9H3D4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.