Research workbench
Crystal structure of trypsin inhibitor 1 from Senna obtusifolia
Analyse Crystal structure of trypsin inhibitor 1 from Senna obtusifolia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KV2
- Type
- protein
- Length
- 710 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.003
- Source
- Senna obtusifolia
- Molecule
- Trypsin inhibitor 1
- EC
- 1.2.3.4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.003 · 4 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trypsin inhibitor 1 (EC 1.2.3.4) | protein | 183 | 3% helix, 46% strand | — |
| B | Trypsin inhibitor 1 (EC 1.2.3.4) | protein | 191 | 4% helix, 43% strand | — |
| D | Trypsin inhibitor 1 (EC 1.2.3.4) | protein | 166 | 0% helix, 48% strand | — |
| C | Trypsin inhibitor 1 (EC 1.2.3.4) | protein | 170 | 2% helix, 49% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.81 | 0.82 | 129 | empty |
| 2 | 143 | 0.50 | 0.79 | 27 | empty |
| 3 | 90 | 0.43 | 0.79 | 19 | empty |
| 4 | 89 | 0.40 | 0.77 | 24 | empty |
| 5 | 120 | 0.37 | 0.74 | 26 | empty |
Interfaces
5 interfaces between chains.
- B–C · 869 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 718 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 670 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 665 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 14 modified, 8 disulfide (engineered, disulfide).
Compared structures
- 6KV2 · Crystal structure of trypsin inhibitor 1 from senna obtusifolia · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6KV2 · PDBe 6KV2
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