Research workbench
Crystal structure of the human thromboxane A2 receptor bound to ramatroban
Analyse Crystal structure of the human thromboxane A2 receptor bound to ramatroban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IIU
- Type
- protein
- Length
- 460 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
- A8X, CLR, ZN
- Pockets
- 5 · best druggability 0.79
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 | 460 | 68% helix, 5% strand | P0ABE7, P21731, P00268 |
Ligands and binding sites
- A8X · 3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 2 copies · 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 | 240 | 0.79 | 0.91 | 32 | A8X |
| 2 | 102 | 0.61 | 0.87 | 20 | empty |
| 3 | 177 | 0.57 | 0.81 | 21 | GOL |
| 4 | 206 | 0.51 | 0.77 | 32 | OLC |
| 5 | 101 | 0.37 | 0.75 | 27 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6IIU · Crystal structure of the human thromboxane A2 receptor bound to ramatroban · 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 6IIU · PDBe 6IIU · UniProt P0ABE7 · UniProt P21731 · UniProt P00268
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