Research workbench
Protease SAPP1P from candida parapsilosis in complex with KB70
Analyse Protease SAPP1P from candida parapsilosis in complex with KB70 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AGB
- Type
- protein
- Length
- 1,376 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Candidapepsin; KB70
- EC
- 3.4.23.24
- UniProt
- B8YPM3
- Ligands
- BOC, NA
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Candidapepsin (EC 3.4.23.24) | protein | 339 | 10% helix, 49% strand | B8YPM3 |
| I, J, K, L | KB70 | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains A, I, B, J, C, K, D, L
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 11 copies · chains A, I, B, C, J, K, D, L
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, D, B, C
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, D
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · chains B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.78 | 0.80 | 86 | PGE, MES |
| 2 | 1003 | 0.78 | 0.80 | 77 | 1PE, MES |
| 3 | 188 | 0.47 | 0.75 | 31 | BOC, NA, PGE |
| 4 | 113 | 0.42 | 0.77 | 16 | PE3 |
| 5 | 51 | 0.41 | 0.83 | 18 | empty |
Interfaces
8 interfaces between chains.
- B–D · 628 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 613 Ų buried · 14 hydrogen bonds · protein-protein
- B–J · 609 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 604 Ų buried · 13 hydrogen bonds · protein-protein
- D–L · 595 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 modified, 4 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 7AGB · Protease Sapp1p from Candida parapsilosis in complex with KB70 · 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 7AGB · PDBe 7AGB · UniProt B8YPM3
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