Research workbench
The refined 1.9 ångströms crystal structure of human alpha-thrombin: interaction with D-phe-pro-arg chloromethylketone and significance of the tyr-pro-pro-TRP insertion segment
Analyse The refined 1.9 ångströms crystal structure of human alpha-thrombin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPB
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 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 | 36 | 31% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 259 | 14% helix, 34% 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 H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.53 | 0.76 | 39 | 0G6 |
| 2 | 94 | 0.43 | 0.78 | 16 | empty |
| 3 | 71 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 1435 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1PPB · The refined 1.9 ångströms crystal structure of human alpha-thrombin: interaction with… · the same entry in another collection · chain L against L, 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 0.91
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 1PPB · PDBe 1PPB · UniProt P00734
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