Research workbench
Crystal structure of tomato inhibitor-II in a ternary complex with subtilisin carlsberg
Analyse Crystal structure of tomato inhibitor-II in a ternary complex with subtilisin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OYV
- Type
- protein
- Length
- 652 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin carlsberg; Wound-induced proteinase inhibitor-II
- EC
- 3.4.21.62
- UniProt
- P00780, P05119
- Ligands
- CA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Subtilisin carlsberg (EC 3.4.21.62) | protein | 274 | 30% helix, 21% strand | P00780 |
| I | Wound-induced proteinase inhibitor-II | protein | 104 | 0% helix, 34% strand | P05119 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.75 | 0.85 | 48 | empty |
| 2 | 197 | 0.50 | 0.76 | 32 | empty |
| 3 | 77 | 0.35 | 0.76 | 16 | empty |
| 4 | 97 | 0.34 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–I · 1007 Ų buried · 18 hydrogen bonds · protein-protein
- B–I · 634 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1OYV · Crystal structure of tomato inhibitor-II in a ternary complex with subtilisin Carlsberg · the same entry in another collection · chain A against A, TM-score 1.00
- P00780 · AlphaFold monomer V2.0 prediction for subtilisin carlsberg (P00780) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P05119 · AlphaFold monomer V2.0 prediction for wound-induced proteinase inhibitor 2 (P05119) · a predicted model of the same protein · chain I against A, TM-score 0.96
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 P00780
- Every structure of UniProt P05119
- Elsewhere: RCSB PDB 1OYV · PDBe 1OYV · UniProt P00780 · UniProt P05119
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