Research workbench
Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex with a 10-mer DNA accggaagtg
Analyse Crystal structure of the DNA binding domain of human transcription factor FLI1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E8I
- Type
- protein + DNA
- Length
- 452 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Friend leukemia integration 1 transcription factor; DNA…
- UniProt
- Q01543
- Ligands
- CA
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Friend leukemia integration 1 transcription factor | protein | 93 | 53% helix, 15% strand | Q01543 |
| B, E, H, K | DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3') | dna | 10 | — | — |
| C, F, I, L | DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3') | dna | 10 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains B, C, F, H, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.71 | 0.76 | 73 | empty |
| 2 | 103 | 0.40 | 0.77 | 13 | empty |
| 3 | 80 | 0.38 | 0.78 | 12 | empty |
| 4 | 58 | 0.36 | 0.79 | 13 | empty |
| 5 | 125 | 0.36 | 0.73 | 21 | empty |
Interfaces
19 interfaces between chains.
- A–G · 884 Ų buried · 10 hydrogen bonds · protein-protein
- D–J · 881 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 557 Ų buried · 9 hydrogen bonds · protein-nucleic
- G–I · 552 Ų buried · 9 hydrogen bonds · protein-nucleic
- J–L · 534 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 5E8I · Crystal structure of the DNA binding domain of human transcription factor FLI1 in complex… · 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 Q01543
- Elsewhere: RCSB PDB 5E8I · PDBe 5E8I · UniProt Q01543
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