MolNFT v1 · #39294 · protein
Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin
2HPQ · Alpha-thrombin (small subunit): “Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin”. X-ray diffraction, 1 ligand (0G7), 6 pockets (best druggability 0.57). MolNFT v1 #39294…
- PDB
- 2HPQ
- Type
- protein
- Length
- 360 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G7
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 30 | 30% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 251 | 13% helix, 36% strand | P00734 |
| P | Prothrombin (EC 3.4.21.5) | protein | 79 | 13% helix, 13% strand | P00734 |
Ligands and binding sites
- 0G7 · D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.57 | 0.80 | 20 | empty |
| 2 | 206 | 0.56 | 0.79 | 37 | 0G7 |
| 3 | 119 | 0.43 | 0.76 | 20 | empty |
| 4 | 85 | 0.36 | 0.75 | 21 | empty |
| 5 | 80 | 0.34 | 0.75 | 13 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1196 Ų buried · 25 hydrogen bonds · protein-protein
- H–P · 834 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 2HPQ · Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with… · the same entry in another collection · chain P against P, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain P against A, TM-score 0.93
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 2HPQ · PDBe 2HPQ · UniProt P00734
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