MolNFT v1 · #172859 · protein
Protease SAPP1P from candida parapsilosis in complex with KB74
7AGC · Candidapepsin: “Protease SAPP1P from candida parapsilosis in complex with KB74”. X-ray diffraction, 2 ligands (BOC, FOR), 13 pockets (best druggability 0.82). MolNFT v1 #172859 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7AGC
- Type
- protein
- Length
- 1,372 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Candidapepsin; KB74
- EC
- 3.4.23.24
- UniProt
- B8YPM3
- Ligands
- BOC, FOR
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Candidapepsin (EC 3.4.23.24) | protein | 339 | 9% helix, 50% strand | B8YPM3 |
| E, I, C, G | KB74 | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains D, E, A, I, B, C, F, G
- FOR · Formyl group · ligand · 4 copies · chains D, E, A, I, B, C, F, G
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, I, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.82 | 0.84 | 84 | FOR |
| 2 | 811 | 0.71 | 0.77 | 78 | empty |
| 3 | 216 | 0.66 | 0.85 | 47 | MES |
| 4 | 460 | 0.59 | 0.74 | 63 | BOC, PGE |
| 5 | 233 | 0.56 | 0.78 | 39 | PEG, FOR |
Interfaces
9 interfaces between chains.
- A–B · 1179 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 12 hydrogen bonds · protein-protein
- F–G · 479 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 477 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 475 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 covalent, 4 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 7AGC · Protease Sapp1p from Candida parapsilosis in complex with KB74 · 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 7AGC · PDBe 7AGC · UniProt B8YPM3
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