MolNFT v1 · #61245 · protein + DNA
Adjacent gata DNA binding
3DFV · DNA (5'- D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*…: “Adjacent gata DNA binding”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.78). MolNFT v1 #61245 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3DFV
- Type
- protein + DNA
- Length
- 152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DC…
- UniProt
- P23772
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y | DNA (5'- D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DC P*DTP*DGP*DC)-3') | dna | 20 | — | — |
| Z | DNA (5'- D(*DAP*DAP*DGP*DCP*DAP*DGP*DAP*DTP*DAP*DAP*DGP*DTP*DCP*DTP*DTP*DAP*DT P*DCP*DAP*DG)-3') | dna | 20 | — | — |
| D, C | Trans-acting T-cell-specific transcription factor gata-3 | protein | 56 | 23% helix, 11% strand | P23772 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.78 | 0.88 | 53 | empty |
| 2 | 58 | 0.44 | 0.83 | 16 | empty |
| 3 | 57 | 0.40 | 0.81 | 17 | empty |
| 4 | 68 | 0.28 | 0.73 | 12 | empty |
Interfaces
6 interfaces between chains.
- Y–Z · 801 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- Z–C · 631 Ų buried · 12 hydrogen bonds · protein-nucleic
- Y–D · 625 Ų buried · 14 hydrogen bonds · protein-nucleic
- Y–C · 588 Ų buried · 9 hydrogen bonds · protein-nucleic
- Z–D · 579 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
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 P23772
- Elsewhere: RCSB PDB 3DFV · PDBe 3DFV · UniProt P23772
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