MolNFT v1 · #16198 · protein
Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes
1NRR · Thrombin light chain: “Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and…”. X-ray diffraction, 1 ligand (0G6), 1 pocket (best druggability 0.52). MolNFT v1 #16198 on…
- PDB
- 1NRR
- Type
- protein
- Length
- 280 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Proteinase-activated receptor 1
- EC
- 3.4.21.5
- UniProt
- P00734, P25116
- Ligands
- 0G6
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 26 | 35% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 249 | 15% helix, 36% strand | P00734 |
| R | Proteinase-activated receptor 1 | protein | 5 | 0% helix, 0% strand | P25116 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.52 | 0.78 | 35 | 0G6 |
Interfaces
2 interfaces between chains.
- L–H · 1075 Ų buried · 25 hydrogen bonds · protein-protein
- H–R · 428 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1NRR · Crystallographic structures of Thrombin complexed with Thrombin receptor peptides… · the same entry in another collection · chain H against H, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
- 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 0.87
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 1NRR · PDBe 1NRR · UniProt P00734 · UniProt P25116
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