Research workbench
Cryoem plasmodium falciparum M18 aspartyl aminopeptidase
Analyse Cryoem plasmodium falciparum M18 aspartyl aminopeptidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PEV
- Type
- protein
- Length
- 5,736 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M18 aspartyl aminopeptidase
- UniProt
- W7K6I8
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | M18 aspartyl aminopeptidase | protein | 478 | 30% helix, 25% strand | W7K6I8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.82 | 0.97 | 25 | empty |
| 2 | 281 | 0.82 | 0.94 | 32 | empty |
| 3 | 264 | 0.82 | 0.94 | 30 | empty |
| 4 | 197 | 0.82 | 0.96 | 29 | empty |
| 5 | 195 | 0.82 | 0.96 | 25 | empty |
Interfaces
30 interfaces between chains.
- A–F · 4371 Ų buried · 46 hydrogen bonds · protein-protein
- K–L · 4356 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 4337 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 4331 Ų buried · 32 hydrogen bonds · protein-protein
- B–I · 4325 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6PEV · CryoEM Plasmodium falciparum M18 aspartyl aminopeptidase · 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 W7K6I8
- Elsewhere: RCSB PDB 6PEV · PDBe 6PEV · UniProt W7K6I8
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