Research workbench
Crystal structure of the second kh domain of FUBP1
Analyse Crystal structure of the second kh domain of FUBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y2D
- Type
- protein
- Length
- 277 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Far upstream element-binding protein 1
- UniProt
- Q96AE4
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Far upstream element-binding protein 1 | protein | 65 | 55% helix, 28% strand | Q96AE4 |
| B | Far upstream element-binding protein 1 | protein | 70 | 51% helix, 26% strand | Q96AE4 |
| C | Far upstream element-binding protein 1 | protein | 68 | 41% helix, 26% strand | Q96AE4 |
| D | Far upstream element-binding protein 1 | protein | 74 | 53% helix, 24% strand | Q96AE4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.68 | 0.83 | 29 | GOL |
| 2 | 154 | 0.53 | 0.79 | 26 | empty |
| 3 | 100 | 0.46 | 0.80 | 19 | empty |
| 4 | 146 | 0.43 | 0.75 | 19 | empty |
| 5 | 124 | 0.43 | 0.76 | 19 | empty |
Interfaces
5 interfaces between chains.
- C–D · 684 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 570 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 512 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6Y2D · Crystal structure of the second KH domain of FUBP1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q96AE4 · AlphaFold monomer V2.0 prediction for far upstream element-binding protein 1 (Q96AE4) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q96AE4
- Elsewhere: RCSB PDB 6Y2D · PDBe 6Y2D · UniProt Q96AE4
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