Research workbench
Protease SAPP1P from candida parapsilosis in complex with KB32
Analyse Protease SAPP1P from candida parapsilosis in complex with KB32 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AGE
- Type
- protein
- Length
- 1,373 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Candidapepsin; Pepstatin
- EC
- 3.4.23.24
- UniProt
- B8YPM3
- Ligands
- BOC, PSA
- Pockets
- 11 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Candidapepsin (EC 3.4.23.24) | protein | 339 | 10% helix, 50% strand | B8YPM3 |
| I, C, G | Pepstatin | protein | 4 | 0% helix, 25% strand | — |
| E | Pepstatin | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains A, I, B, C, D, E, F, G
- PSA · 3-hydroxy-4-amino-5-phenylpentanoic acid · ligand · 3 copies · chains A, I, B, C, F, G
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.44 | 0.75 | 37 | BOC, PSA, PEG |
| 2 | 159 | 0.42 | 0.74 | 28 | BOC, PSA, PEG |
| 3 | 148 | 0.42 | 0.74 | 38 | BOC, PSA |
| 4 | 68 | 0.35 | 0.77 | 17 | empty |
| 5 | 80 | 0.31 | 0.73 | 17 | BOC, PEG |
Interfaces
4 interfaces between chains.
- D–E · 577 Ų buried · 15 hydrogen bonds · protein-protein
- A–I · 481 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 478 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 477 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 covalent, 5 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 7AGE · Protease Sapp1p from Candida parapsilosis in complex with KB32 · 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
- Every structure of UniProt B8YPM3
- Elsewhere: RCSB PDB 7AGE · PDBe 7AGE · UniProt B8YPM3
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