MolNFT v1 · #167289 · protein + DNA
Crystal structure of the DNA binding domains of human FLI1 and RUNX2 in complex with 16-mer DNA cagaggatgtggcttc
6VG8 · Friend leukemia integration 1 transcription factor: “Crystal structure of the DNA binding domains of human FLI1 and RUNX2 in complex with 16-mer DNA…”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #167289 on…
- PDB
- 6VG8
- Type
- protein + DNA
- Length
- 248 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Friend leukemia integration 1 transcription factor; DNA (5'…
- UniProt
- Q01543, Q13950
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Friend leukemia integration 1 transcription factor | protein | 96 | 39% helix, 13% strand | Q01543 |
| B | DNA (5'- D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3') | dna | 16 | — | — |
| C | DNA (5'- D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3') | dna | 16 | — | — |
| D | Runt-related transcription factor 2 | protein | 120 | 0% helix, 33% strand | Q13950 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.95 | 22 | empty |
| 2 | 374 | 0.60 | 0.77 | 26 | empty |
| 3 | 209 | 0.57 | 0.80 | 29 | empty |
| 4 | 165 | 0.55 | 0.81 | 19 | empty |
| 5 | 123 | 0.46 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 727 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–C · 505 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 476 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 436 Ų buried · 8 hydrogen bonds · protein-nucleic
- C–D · 407 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6VG8 · Crystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13950 · AlphaFold monomer V2.0 prediction for runt-related transcription factor 2 (Q13950) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q01543 · AlphaFold monomer V2.0 prediction for friend leukemia integration 1 transcription factor… · a predicted model of the same protein · chain A against A, TM-score 0.87
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
- Every structure of UniProt Q13950
- Elsewhere: RCSB PDB 6VG8 · PDBe 6VG8 · UniProt Q01543 · UniProt Q13950
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