Research workbench
Crystal structure of the subtilisin CARLSBERG:OMTKY3 complex
Analyse Crystal structure of the subtilisin CARLSBERG:OMTKY3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YU6
- Type
- protein
- Length
- 649 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Subtilisin carlsberg; Ovomucoid
- EC
- 3.4.21.62
- UniProt
- P00780, P68390
- Ligands
- CA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 22% 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 |
| C | Ovomucoid | protein | 51 | 20% helix, 24% strand | P68390 |
| D | Ovomucoid | protein | 50 | 22% helix, 24% strand | P68390 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.72 | 0.76 | 66 | empty |
| 2 | 209 | 0.55 | 0.79 | 42 | empty |
| 3 | 167 | 0.49 | 0.77 | 31 | empty |
| 4 | 162 | 0.41 | 0.73 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–C · 746 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 704 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 112 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1YU6 · Crystal Structure of the Subtilisin Carlsberg:OMTKY3 Complex · 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
- P68390 · AlphaFold monomer V2.0 prediction for ovomucoid (P68390) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P68390
- Elsewhere: RCSB PDB 1YU6 · PDBe 1YU6 · UniProt P00780 · UniProt P68390
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