MolNFT v1 · #16199 · protein
Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and novel binding modes
1NRS · Alpha-thrombin (small subunit): “Crystallographic structures of thrombin complexed with thrombin receptor peptides: existence of expected and…”. X-ray diffraction, 2 pockets (best druggability 0.43). MolNFT v1 #16199 on GenesisL1…
- PDB
- 1NRS
- Type
- protein
- Length
- 292 residues
- Chains
- 4
- 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, P09945
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 252 | 16% helix, 37% strand | P00734 |
| R | Receptor based peptide nrp | protein | 4 | 0% helix, 50% strand | — |
| I | Hirugen | protein | 9 | 0% helix, 0% strand | P09945 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.43 | 0.76 | 21 | empty |
| 2 | 54 | 0.31 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1117 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 598 Ų buried · 8 hydrogen bonds · protein-protein
- H–R · 478 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1NRS · Crystallographic structures of thrombin complexed with thrombin receptor peptides… · the same entry in another collection · chain L against L, TM-score 1.00
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.48
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 P09945
- Elsewhere: RCSB PDB 1NRS · PDBe 1NRS · UniProt P00734 · UniProt P09945
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