Research workbench
Crystal structure of the human DOK1 ptb domain
Analyse Crystal structure of the human DOK1 ptb domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V76
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Docking protein 1
- UniProt
- Q53TY2
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Docking protein 1 | protein | 99 | 22% helix, 46% strand | Q53TY2 |
| B, C | Docking protein 1 | protein | 102 | 24% helix, 44% strand | Q53TY2 |
| D | Docking protein 1 | protein | 99 | 21% helix, 45% strand | Q53TY2 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · chains A
- GOL · Glycerol · additive · chains C
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 | 609 | 0.63 | 0.74 | 63 | PGE |
| 2 | 60 | 0.37 | 0.79 | 15 | empty |
| 3 | 52 | 0.23 | 0.72 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 434 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 268 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 236 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 49 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2V76 · Crystal structure of the human dok1 PTB domain · the same entry in another collection · chain A against A, TM-score 1.00
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 Q53TY2
- Elsewhere: RCSB PDB 2V76 · PDBe 2V76 · UniProt Q53TY2
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