Research workbench
Crystal structure of PRAPE1
Analyse Crystal structure of PRAPE1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JH9
- Type
- protein
- Length
- 1,900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar aminopeptidase 1
- EC
- 3.4.11.22
- UniProt
- P14904
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 475 | 34% helix, 24% strand | P14904 |
| B | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 477 | 33% helix, 25% strand | P14904 |
| C | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 473 | 34% helix, 23% strand | P14904 |
| D | Vacuolar aminopeptidase 1 (EC 3.4.11.22) | protein | 475 | 33% helix, 23% strand | P14904 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.84 | 0.96 | 44 | empty |
| 2 | 441 | 0.68 | 0.80 | 69 | CAC |
| 3 | 94 | 0.60 | 0.88 | 23 | CAC |
| 4 | 133 | 0.58 | 0.84 | 30 | CAC |
| 5 | 302 | 0.58 | 0.77 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3398 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 3389 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 1743 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P14904
- Elsewhere: RCSB PDB 5JH9 · PDBe 5JH9 · UniProt P14904
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.