Research workbench
X-ray crystal structure and specificity of the plasmodium falciparum malaria aminopeptidase
Analyse X-ray crystal structure and specificity of the plasmodium falciparum malaria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EME
- Type
- protein
- Length
- 1,891 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M18 aspartyl aminopeptidase
- EC
- 3.4.11.21
- UniProt
- Q8I2J3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M18 aspartyl aminopeptidase (EC 3.4.11.21) | protein | 474 | 35% helix, 27% strand | Q8I2J3 |
| B | M18 aspartyl aminopeptidase (EC 3.4.11.21) | protein | 473 | 37% helix, 26% strand | Q8I2J3 |
| C | M18 aspartyl aminopeptidase (EC 3.4.11.21) | protein | 475 | 37% helix, 26% strand | Q8I2J3 |
| D | M18 aspartyl aminopeptidase (EC 3.4.11.21) | protein | 469 | 37% helix, 26% strand | Q8I2J3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.85 | 0.94 | 48 | empty |
| 2 | 220 | 0.76 | 0.90 | 31 | empty |
| 3 | 57 | 0.73 | 0.99 | 29 | empty |
| 4 | 64 | 0.73 | 0.98 | 29 | empty |
| 5 | 56 | 0.72 | 0.99 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3795 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2285 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2253 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2251 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4EME · X-ray crystal structure and specificity of the Plasmodium falciparum malaria… · 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 Q8I2J3
- Elsewhere: RCSB PDB 4EME · PDBe 4EME · UniProt Q8I2J3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.