Research workbench
Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin
Analyse Structures of the noncovalent complexes of human and bovine prothrombin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HPP
- Type
- protein
- Length
- 360 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin light chain; Alpha-thrombin heavy chain; Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734, P00735
- Ligands
- 0G7
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin light chain (EC 3.4.21.5) | protein | 30 | 30% helix, 0% strand | P00734 |
| H | Alpha-thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| P | Prothrombin (EC 3.4.21.5) | protein | 79 | 0% helix, 18% strand | P00735 |
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 | 203 | 0.53 | 0.78 | 38 | 0G7 |
| 2 | 126 | 0.51 | 0.81 | 22 | empty |
| 3 | 133 | 0.41 | 0.75 | 21 | empty |
| 4 | 66 | 0.30 | 0.74 | 18 | empty |
| 5 | 52 | 0.28 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1194 Ų buried · 21 hydrogen bonds · protein-protein
- H–P · 858 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent, 1 isopeptide (disulfide, covalent ligand, isopeptide).
Compared structures
- 2HPP · Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with… · 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 P against A, TM-score 0.93
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H 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
- Every structure of UniProt P00735
- Elsewhere: RCSB PDB 2HPP · PDBe 2HPP · UniProt P00734 · UniProt P00735
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.