MolNFT v1 · #172860 · protein
Protease SAPP1P from candida parapsilosis in complex with KB75
7AGD · Candidapepsin: “Protease SAPP1P from candida parapsilosis in complex with KB75”. X-ray diffraction, 4 ligands (BOC, PSA, FOR), 12 pockets (best druggability 0.77). MolNFT v1 #172860 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7AGD
- Type
- protein
- Length
- 1,375 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Candidapepsin; KB75
- EC
- 3.4.23.24
- UniProt
- B8YPM3
- Ligands
- BOC, PSA, FOR, NA
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 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, 50% strand | B8YPM3 |
| I, J, L | KB75 | protein | 5 | 0% helix, 40% strand | — |
| K | KB75 | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- BOC · Tert-butyl hydrogen carbonate · ligand · 4 copies · chains A, I, B, J, C, K, D, L
- PSA · 3-hydroxy-4-amino-5-phenylpentanoic acid · ligand · chains C, K
- FOR · Formyl group · ligand · chains B, J
- NA · Sodium ion · metal · chains D
- PGE · Triethylene glycol · additive · 3 copies · chains B, C, D
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, I
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.77 | 0.80 | 77 | 1PE |
| 2 | 998 | 0.77 | 0.79 | 83 | PGE |
| 3 | 177 | 0.47 | 0.76 | 40 | BOC, FOR |
| 4 | 180 | 0.46 | 0.75 | 33 | BOC |
| 5 | 106 | 0.41 | 0.76 | 28 | empty |
Interfaces
8 interfaces between chains.
- A–I · 640 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 634 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 604 Ų buried · 13 hydrogen bonds · protein-protein
- D–L · 603 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 7 modified, 6 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 7AGD · Protease Sapp1p from Candida parapsilosis in complex with KB75 · 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 7AGD · PDBe 7AGD · UniProt B8YPM3
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