Research workbench
Structure of TRPA1 modified by bodipy-iodoacetamide with bound calcium, lmng
Analyse Structure of TRPA1 modified by bodipy-iodoacetamide with bound calcium, lmng in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V9V
- Type
- protein
- Length
- 2,388 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily a member 1
- UniProt
- O75762
- Ligands
- QT4, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | Transient receptor potential cation channel subfamily a member 1 | protein | 597 | 61% helix, 2% strand | O75762 |
Ligands and binding sites
- QT4 · ~{N}-[[2,2-bis(fluoranyl)-10,12-dimethyl-1,3-diaza-2$l^{4}-boratricyclo[7.3.0.0^{3,7}]dodeca-4,6,9,11-tetraen-4-yl]methyl]ethanamide · ligand · 4 copies · chains A, B, D, C
- CA · Calcium ion · metal · 4 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.83 | 0.88 | 54 | empty |
| 2 | 900 | 0.73 | 0.77 | 95 | empty |
| 3 | 781 | 0.70 | 0.76 | 66 | CA |
| 4 | 935 | 0.70 | 0.75 | 78 | empty |
| 5 | 715 | 0.69 | 0.76 | 56 | empty |
Interfaces
6 interfaces between chains.
- D–C · 3552 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3550 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3544 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 3531 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6V9V · Structure of TRPA1 modified by Bodipy-iodoacetamide with bound calcium, LMNG · the same entry in another collection · chain A against A, TM-score 1.00
- O75762 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.83
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 O75762
- Elsewhere: RCSB PDB 6V9V · PDBe 6V9V · UniProt O75762
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