Research workbench
Structure of the two tandem tudor domains and a new identified KH0 domain from human fragile X mental retardation protein
Analyse Structure of the two tandem tudor domains and a new identified KH0 domain from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OVA
- Type
- protein
- Length
- 799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragile X mental retardation protein 1
- UniProt
- Q06787
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Fragile X mental retardation protein 1 | protein | 200 | 28% helix, 36% strand | Q06787 |
| C | Fragile X mental retardation protein 1 | protein | 199 | 24% helix, 36% strand | Q06787 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.77 | 0.79 | 103 | TRS |
| 2 | 382 | 0.70 | 0.82 | 45 | empty |
| 3 | 131 | 0.45 | 0.77 | 16 | empty |
| 4 | 98 | 0.43 | 0.78 | 17 | empty |
| 5 | 60 | 0.31 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 520 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 454 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 422 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OVA · Structure of the two tandem Tudor domains and a new identified KH0 domain from human… · the same entry in another collection · chain D against D, TM-score 1.00
- Q06787 · AlphaFold monomer V2.0 prediction for synaptic functional regulator FMR1 (Q06787) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q06787
- Elsewhere: RCSB PDB 4OVA · PDBe 4OVA · UniProt Q06787
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