Research workbench
Crystal structure of the human thromboxane A2 receptor bound to daltroban
Analyse Crystal structure of the human thromboxane A2 receptor bound to daltroban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IIV
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,THROMBOXANE A2 RECEPTOR,RUBREDOXIN, thromboxane A2 receptor
- UniProt
- P0ABE7, P21731, P00268
- Ligands
- A90, CLR, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562,THROMBOXANE A2 RECEPTOR,RUBREDOXIN, thromboxane A2 receptor | protein | 461 | 68% helix, 5% strand | P0ABE7, P21731, P00268 |
Ligands and binding sites
- A90 · 2-[4-[2-[(4-chlorophenyl) sulfonylamino]ethyl]phenyl]ethanoic acid · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.81 | 0.94 | 33 | A90 |
| 2 | 149 | 0.54 | 0.81 | 23 | GOL |
| 3 | 195 | 0.53 | 0.78 | 25 | empty |
| 4 | 100 | 0.52 | 0.83 | 23 | empty |
| 5 | 158 | 0.43 | 0.74 | 32 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6IIV · Crystal structure of the human thromboxane A2 receptor bound to daltroban · the same entry in another collection · chain A against A, TM-score 1.00
- P21731 · AlphaFold monomer V2.0 prediction for thromboxane A2 receptor (P21731) · a predicted model of the same protein · chain A against A, TM-score 0.67
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.23
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.12
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 P0ABE7
- Every structure of UniProt P21731
- Every structure of UniProt P00268
- Elsewhere: RCSB PDB 6IIV · PDBe 6IIV · UniProt P0ABE7 · UniProt P21731 · UniProt P00268
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