Research workbench
Metal dependent activation of plasmodium falciparum M17 aminopeptidase, spacegroup P22121 after crystals soaked with ZN2+
Analyse Metal dependent activation of plasmodium falciparum M17 aminopeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T3V
- Type
- protein
- Length
- 3,092 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 leucyl aminopeptidase
- EC
- 3.4.11.1
- UniProt
- Q8IL11
- Ligands
- ZN, CO3, SO4
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 519 | 34% helix, 22% strand | Q8IL11 |
| B, C | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 518 | 35% helix, 22% strand | Q8IL11 |
| D | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 517 | 36% helix, 22% strand | Q8IL11 |
| E | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 511 | 35% helix, 22% strand | Q8IL11 |
| F | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 509 | 36% helix, 21% strand | Q8IL11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.73 | 0.78 | 70 | CO3 |
| 2 | 839 | 0.73 | 0.78 | 67 | CO3 |
| 3 | 830 | 0.72 | 0.77 | 70 | empty |
| 4 | 822 | 0.72 | 0.77 | 71 | CO3 |
| 5 | 795 | 0.71 | 0.77 | 98 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1522 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1521 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1520 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1499 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1480 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7T3V · Metal dependent activation of Plasmodium falciparum M17 aminopeptidase, spacegroup P22121… · 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 Q8IL11
- Elsewhere: RCSB PDB 7T3V · PDBe 7T3V · UniProt Q8IL11
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