Research workbench
Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide motif
Analyse Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AY6
- Type
- protein
- Length
- 291 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- 1ZV
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 31% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 35% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P01050 |
Ligands and binding sites
- 1ZV · amino({3-[(3R,5R,14S,16S,21aR)-5,14-dihydroxy-1,4,17-trioxo-16-(2-phenylethyl)icosahydro-1H-pyrrolo[1,2-d][1,4,7,11]tetraazacyclononadecin-3-yl]propyl}amino)methaniminium · 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 | 294 | 0.56 | 0.76 | 41 | 1ZV |
| 2 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1223 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 605 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1AY6 · Thrombin inhibitor from theonalla, cyclotheanamide-based macrocyclic tripeptide motif · 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 0.92
- P01050 · AlphaFold monomer V2.0 prediction for hirudin variant-1 (P01050) · a predicted model of the same protein · chain I against A, TM-score 0.56
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 P01050
- Elsewhere: RCSB PDB 1AY6 · PDBe 1AY6 · UniProt P00734 · UniProt P01050
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