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The co-crystal structure of unliganded bovine alpha- thrombin and prethrombin-2: movement of the yppw segment and active site residues upon ligand binding
Analyse The co-crystal structure of unliganded bovine alpha- thrombin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MKX
- Type
- protein
- Length
- 571 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Prethrombin-2
- EC
- 3.4.21.5
- UniProt
- P00735
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 29 | 38% helix, 0% strand | P00735 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 255 | 13% helix, 34% strand | P00735 |
| K | Prethrombin-2 (EC 3.4.21.5) | protein | 287 | 16% helix, 30% strand | P00735 |
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 | 831 | 0.77 | 0.80 | 77 | empty |
| 2 | 94 | 0.39 | 0.76 | 17 | empty |
| 3 | 66 | 0.37 | 0.78 | 14 | empty |
| 4 | 65 | 0.36 | 0.78 | 15 | empty |
| 5 | 71 | 0.31 | 0.74 | 13 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1215 Ų buried · 19 hydrogen bonds · protein-protein
- H–K · 713 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1MKX · The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement… · the same entry in another collection · chain L against L, TM-score 1.00
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 P00735
- Elsewhere: RCSB PDB 1MKX · PDBe 1MKX · UniProt P00735
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