Research workbench
Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes
Analyse Crystallographic structures of thrombin complexed with thrombin receptor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NRP
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Receptor based peptide…
- EC
- 3.4.21.5
- UniProt
- P00734, P25116
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 29 | 24% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 257 | 7% helix, 30% strand | P00734 |
| R | Receptor based peptide NR'S | protein | 10 | 0% helix, 10% strand | P25116 |
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.49 | 0.77 | 26 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1062 Ų buried · 16 hydrogen bonds · protein-protein
- H–R · 582 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 1NRP · Crystallographic structures of thrombin complexed with thrombin receptor peptides… · the same entry in another collection · chain L against L, TM-score 1.00
- P25116 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 1 (P25116) · a predicted model of the same protein · chain R against A, TM-score 0.36
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 1NRP · PDBe 1NRP · UniProt P00734 · UniProt P25116
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