Research workbench
Structure of human alpha-thrombin Y225P mutant bound to D-phe-pro-arg- chloromethylketone
Analyse Structure of human alpha-thrombin Y225P mutant bound to D-phe-pro-arg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1THP
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (thrombin light chain); Protein (thrombin heavy chain)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (thrombin light chain) | protein | 27 | 41% helix, 0% strand | P00734 |
| B | Protein (thrombin heavy chain) (EC 3.4.21.5) | protein | 249 | 13% helix, 35% strand | P00734 |
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 B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.60 | 0.92 | 19 | empty |
| 2 | 117 | 0.49 | 0.80 | 24 | 0G6 |
| 3 | 62 | 0.34 | 0.77 | 16 | empty |
| 4 | 69 | 0.31 | 0.75 | 18 | empty |
| 5 | 62 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1THP · Structure of human alpha-thrombin Y225P mutant bound to D-phe-pro-arg-chloromethylketone · the same entry in another collection · chain B against B, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 1THP · PDBe 1THP · UniProt P00734
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