Research workbench
Crystal structure of the DAP12 transmembrane domain in lipid cubic phase
Analyse Crystal structure of the DAP12 transmembrane domain in lipid cubic phase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WO1
- Type
- protein
- Length
- 128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyro protein tyrosine kinase-binding protein
- UniProt
- O43914
- Ligands
- CA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 84% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tyro protein tyrosine kinase-binding protein | protein | 32 | 84% helix, 3% strand | O43914 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B, D
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.71 | 0.84 | 34 | CA, OLC |
| 2 | 131 | 0.57 | 0.83 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–C · 583 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 574 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 283 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 281 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 272 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4WO1 · Crystal structure of the DAP12 transmembrane domain in lipid cubic phase · the same entry in another collection · chain A against A, TM-score 1.00
- O43914 · AlphaFold monomer V2.0 prediction for tyro protein tyrosine kinase- binding protein… · a predicted model of the same protein · chain A against A, TM-score 0.78
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 O43914
- Elsewhere: RCSB PDB 4WO1 · PDBe 4WO1 · UniProt O43914
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