Research workbench
Crystal structure of interleukin enhancer-binding factor 1 bound to DNA
Analyse Crystal structure of interleukin enhancer-binding factor 1 bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C6Y
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Forkhead box protein K2; Interleukin 2 promotor
- UniProt
- Q01167
- Ligands
- MG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Forkhead box protein K2 | protein | 98 | 46% helix, 10% strand | Q01167 |
| B | Forkhead box protein K2 | protein | 95 | 46% helix, 11% strand | Q01167 |
| C | Interleukin 2 promotor | dna | 16 | — | — |
| D | Interleukin 2 promotor | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.60 | 0.76 | 41 | empty |
| 2 | 94 | 0.45 | 0.80 | 23 | empty |
| 3 | 78 | 0.35 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 670 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- A–D · 646 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 541 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–D · 446 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 254 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 2C6Y · Crystal structure of interleukin enhancer-binding factor 1 bound to DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q01167 · AlphaFold monomer V2.0 prediction for forkhead box protein K2 (Q01167) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q01167
- Elsewhere: RCSB PDB 2C6Y · PDBe 2C6Y · UniProt Q01167
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