Research workbench
Human alpha thrombin inhibited by rppgf and hirugen
Analyse Human alpha thrombin inhibited by rppgf and hirugen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NY2
- Type
- protein
- Length
- 309 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirugen; Inhibitor peptide rppgf
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Thrombin light chain (EC 3.4.21.5) | protein | 36 | 19% helix, 3% strand | P00734 |
| 2 | Thrombin heavy chain (EC 3.4.21.5) | protein | 259 | 14% helix, 35% strand | P00734 |
| 3 | Hirugen | protein | 10 | 0% helix, 0% strand | P28504 |
| 4 | Inhibitor peptide rppgf | protein | 4 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.43 | 0.83 | 19 | empty |
| 2 | 103 | 0.37 | 0.74 | 20 | empty |
| 3 | 64 | 0.36 | 0.78 | 17 | empty |
| 4 | 54 | 0.27 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- 1–2 · 1392 Ų buried · 28 hydrogen bonds · protein-protein
- 2–3 · 612 Ų buried · 6 hydrogen bonds · protein-protein
- 2–4 · 377 Ų buried · 12 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 1NY2 · PDBe 1NY2 · UniProt P00734 · UniProt P28504
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