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Crystal structure of the TDRD2 extended tudor domain in complex with an antibody fragment and the PIWIL1 peptide
Analyse Crystal structure of the TDRD2 extended tudor domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PI7
- Type
- protein
- Length
- 1,250 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tudor and kh domain-containing protein; Uncharacterized protein; Fab antigen-binding…
- UniProt
- Q9Y2W6
- Ligands
- UNX
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Tudor and kh domain-containing protein | protein | 192 | 22% helix, 39% strand | Q9Y2W6 |
| B, E | Uncharacterized protein | protein | 211 | 7% helix, 51% strand | — |
| C, F | Fab antigen-binding fragment | protein | 219 | 9% helix, 49% strand | — |
| G | Piwi-like protein 1 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 5 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.71 | 0.92 | 34 | empty |
| 2 | 104 | 0.67 | 0.91 | 22 | empty |
| 3 | 289 | 0.64 | 0.80 | 30 | empty |
| 4 | 203 | 0.63 | 0.83 | 29 | empty |
| 5 | 173 | 0.59 | 0.82 | 27 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1672 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1635 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 830 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 821 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 500 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 6PI7 · Crystal structure of the TDRD2 extended Tudor domain in complex with an antibody fragment… · the same entry in another collection · chain G against G, TM-score 1.00
- Q9Y2W6 · AlphaFold monomer V2.0 prediction for tudor and kh domain-containing protein (Q9Y2W6) · a predicted model of the same protein · chain A 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 Q9Y2W6
- Elsewhere: RCSB PDB 6PI7 · PDBe 6PI7 · UniProt Q9Y2W6
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