Research workbench
Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin
Analyse Structure of a retro-binding peptide inhibitor complexed with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDT
- Type
- protein
- Length
- 303 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirugen peptide
- EC
- 3.4.21.5
- UniProt
- P00734, P28507
- Ligands
- 0E7
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 33 | 30% helix, 0% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 259 | 12% helix, 35% strand | P00734 |
| P | Hirugen peptide | protein | 11 | 0% helix, 0% strand | P28507 |
Ligands and binding sites
- 0E7 · methyl N-(4-carbamimidamidobutanoyl)-L-phenylalanyl-L-allothreonyl-L-phenylalaninate · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.59 | 0.77 | 48 | 0E7 |
| 2 | 111 | 0.39 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1280 Ų buried · 20 hydrogen bonds · protein-protein
- H–P · 620 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1HDT · Structure of a retro-binding peptide inhibitor complexed with human alpha-thrombin · 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
- P28507 · AlphaFold monomer V2.0 prediction for hirudin-3A (P28507) · a predicted model of the same protein · chain P against A, TM-score 0.45
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 P28507
- Elsewhere: RCSB PDB 1HDT · PDBe 1HDT · UniProt P00734 · UniProt P28507
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