Research workbench
Crystal structure of thrombin bound to the extracellular fragment of PAR1
Analyse Crystal structure of thrombin bound to the extracellular fragment of PAR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BEF
- Type
- protein
- Length
- 604 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Proteinase-activated receptor 1
- EC
- 3.4.21.5
- UniProt
- P00734, P25116
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 44 | 36% helix, 0% strand | P00734 |
| B, E | Prothrombin (EC 3.4.21.5) | protein | 251 | 12% helix, 34% strand | P00734 |
| C | Proteinase-activated receptor 1 | protein | 9 | 0% helix, 0% strand | P25116 |
| D | Prothrombin (EC 3.4.21.5) | protein | 42 | 45% helix, 0% strand | P00734 |
| F | Proteinase-activated receptor 1 | protein | 7 | 0% helix, 0% strand | P25116 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.66 | 0.78 | 48 | empty |
| 2 | 239 | 0.56 | 0.78 | 31 | empty |
| 3 | 242 | 0.54 | 0.77 | 33 | empty |
| 4 | 54 | 0.35 | 0.78 | 20 | empty |
| 5 | 60 | 0.30 | 0.75 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1697 Ų buried · 36 hydrogen bonds · protein-protein
- D–E · 1669 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 390 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 285 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 194 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3BEF · Crystal structure of thrombin bound to the extracellular fragment of PAR1 · the same entry in another collection · chain F against F, TM-score 1.00
- P25116 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 1 (P25116) · a predicted model of the same protein · chain F against A, TM-score 0.56
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 P00734
- Every structure of UniProt P25116
- Elsewhere: RCSB PDB 3BEF · PDBe 3BEF · UniProt P00734 · UniProt P25116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.