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Structure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
Analyse Structure of the m17 leucyl aminopeptidase from malaria complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R76
- Type
- protein
- Length
- 6,155 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Plasmodium falciparum fcb1/columbia
- Molecule
- M17 family aminopeptidase
- Ligands
- R5X, ZN, CO3, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.5 · 12 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M17 family aminopeptidase | protein | 515 | 35% helix, 22% strand | — |
| B | M17 family aminopeptidase | protein | 511 | 35% helix, 22% strand | — |
| C | M17 family aminopeptidase | protein | 518 | 35% helix, 22% strand | — |
| D | M17 family aminopeptidase | protein | 514 | 36% helix, 22% strand | — |
| E | M17 family aminopeptidase | protein | 510 | 35% helix, 22% strand | — |
| F | M17 family aminopeptidase | protein | 509 | 35% helix, 21% strand | — |
| G | M17 family aminopeptidase | protein | 517 | 34% helix, 22% strand | — |
| H | M17 family aminopeptidase | protein | 515 | 34% helix, 22% strand | — |
| I | M17 family aminopeptidase | protein | 516 | 34% helix, 22% strand | — |
| J | M17 family aminopeptidase | protein | 511 | 36% helix, 22% strand | — |
| K | M17 family aminopeptidase | protein | 509 | 35% helix, 22% strand | — |
| L | M17 family aminopeptidase | protein | 510 | 34% helix, 22% strand | — |
Ligands and binding sites
- R5X · 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 15 copies · chains B, 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 | 1158 | 0.77 | 0.79 | 130 | empty |
| 2 | 1131 | 0.75 | 0.78 | 123 | empty |
| 3 | 886 | 0.74 | 0.78 | 72 | CO3, R5X |
| 4 | 891 | 0.74 | 0.78 | 68 | CO3, R5X |
| 5 | 881 | 0.74 | 0.78 | 72 | R5X |
Interfaces
26 interfaces between chains.
- H–I · 1506 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1505 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1496 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1494 Ų buried · 24 hydrogen bonds · protein-protein
- G–I · 1488 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4R76 · Structure of the M17 leucyl aminopeptidase from malaria complexed with a hydroxamic… · 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
- Elsewhere: RCSB PDB 4R76 · PDBe 4R76
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