Research workbench
The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer
Analyse The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HUT
- Type
- protein + DNA
- Length
- 304 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3'; Alpha-thrombin light chain…
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G7
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA 5'-D(*GP*GP*TP*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3' | dna | 15 | — | — |
| L | Alpha-thrombin light chain (EC 3.4.21.5) | protein | 36 | 11% helix, 3% strand | P00734 |
| H | Alpha-thrombin heavy chain (EC 3.4.21.5) | protein | 253 | 11% helix, 29% 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.61 | 0.78 | 49 | 0G7 |
Interfaces
2 interfaces between chains.
- L–H · 1491 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 504 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1HUT · The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer · the same entry in another collection · chain D against D, 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 1HUT · PDBe 1HUT · UniProt P00734
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