Research workbench
Thrombin inhibitor complex
Analyse Thrombin inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YPG
- Type
- protein
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- UIR
- Pockets
- 1 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 15% helix, 35% strand | P00734 |
| I | Hirudin | protein | 10 | 30% helix, 0% strand | P28504 |
Ligands and binding sites
- UIR · (1r,3as,4r,8as,8br)-4-(2-benzo[1,3]dioxol-5-yl-1-cyclopropyl-3-oxo-decahydro-pyrrolo[3,4-a]pyrrolizin-4-yl)-benzamidine · 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 | 286 | 0.54 | 0.76 | 39 | UIR |
Interfaces
2 interfaces between chains.
- L–H · 1108 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 620 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
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 P28504
- Elsewhere: RCSB PDB 1YPG · PDBe 1YPG · UniProt P00734 · UniProt P28504
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