MolNFT v1 · #123800 · protein + DNA
Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA gaccggaagtg
5JVT · Friend leukemia integration 1 transcription factor: “Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with an 11-mer DNA…”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.59).…
- PDB
- 5JVT
- Type
- protein + DNA
- Length
- 348 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Friend leukemia integration 1 transcription factor; DNA…
- UniProt
- Q01543
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Friend leukemia integration 1 transcription factor | protein | 96 | 45% helix, 13% strand | Q01543 |
| B, E, H | DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3') | dna | 11 | — | — |
| C, F, I | DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3') | dna | 11 | — | — |
| D, G | Friend leukemia integration 1 transcription factor | protein | 93 | 47% helix, 13% strand | Q01543 |
Ligands and binding sites
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 | 398 | 0.59 | 0.76 | 25 | PO4 |
| 2 | 116 | 0.38 | 0.75 | 15 | empty |
| 3 | 117 | 0.36 | 0.74 | 16 | empty |
| 4 | 88 | 0.32 | 0.74 | 14 | empty |
Interfaces
17 interfaces between chains.
- D–G · 845 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 8 hydrogen bonds · protein-nucleic
- G–I · 552 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–F · 550 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 485 Ų buried · 42 hydrogen bonds · nucleic-nucleic
Compared structures
- 5JVT · Crystal structure of the DNA binding domain of transcription factor FLI1 in complex with… · the same entry in another collection · chain I against I, TM-score 1.00
- Q01543 · AlphaFold monomer V2.0 prediction for friend leukemia integration 1 transcription factor… · a predicted model of the same protein · chain G 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 Q01543
- Elsewhere: RCSB PDB 5JVT · PDBe 5JVT · UniProt Q01543
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