MolNFT v1 · #160363 · protein
Crystal structure of the TDRD2 extended tudor domain in complex with an antibody fragment and the PIWIL1 peptide
6PI7 · Tudor and kh domain-containing protein: “Crystal structure of the TDRD2 extended tudor domain in complex with an antibody fragment and the PIWIL1…”. X-ray diffraction, 1 ligand (UNX), 15 pockets (best druggability 0.71). MolNFT v1…
- 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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