Research workbench
Human alpha-thrombin complexed with a peptidyl pyridinium methyl ketone containing bivalent inhibitor
Analyse Human alpha-thrombin complexed with a peptidyl pyridinium methyl ketone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HBT
- Type
- protein
- Length
- 292 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); P596 inhibitor peptide
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- AR0
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% 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 | 249 | 14% helix, 36% strand | P00734 |
| I | P596 inhibitor peptide | protein | 16 | 19% helix, 0% strand | — |
Ligands and binding sites
- AR0 · 4-amino-1-{[amino(iminio)methyl]amino}-6-[4-(carboxymethyl)pyridinium-1-yl]-1,2,3,4,6-pentadeoxy-D-erythro-hexitol · ligand · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 57 | 0.37 | 0.79 | 16 | AR0 |
| 2 | 51 | 0.25 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1118 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 949 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 covalent, 2 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 1HBT · Human alpha-thrombin complexed with a peptidyl pyridinium methyl ketone containing… · the same entry in another collection · chain L against L, TM-score 1.00
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
- Elsewhere: RCSB PDB 1HBT · PDBe 1HBT · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.