MolNFT v1 · #127810 · protein
Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in complex with the inhibitor pepstatin a
5N7Q · Putative cathepsin D: “Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in complex with the inhibitor…”. X-ray diffraction, 1 ligand (IVA), 4 pockets (best druggability 0.72). MolNFT v1 #127810 on…
- PDB
- 5N7Q
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cathepsin D; Pepstatin a
- UniProt
- V5HCK7
- Ligands
- IVA
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative cathepsin D | protein | 337 | 15% helix, 46% strand | V5HCK7 |
| I, J | Pepstatin a | protein | 5 | 0% helix, 40% strand | — |
Ligands and binding sites
- IVA · Isovaleric acid · ligand · 2 copies · chains A, I, B, J
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.72 | 0.76 | 103 | empty |
| 2 | 196 | 0.48 | 0.75 | 28 | IVA |
| 3 | 161 | 0.43 | 0.74 | 24 | IVA |
| 4 | 59 | 0.29 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–I · 587 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 579 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 modified, 2 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 5N7Q · Crystal structure of mature cathepsin D from the tick ixodes ricinus (IRCD1) in complex… · 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 V5HCK7
- Elsewhere: RCSB PDB 5N7Q · PDBe 5N7Q · UniProt V5HCK7
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