Research workbench
Metal dependent activation of plasmodium falciparum M17 aminopeptidase (inactive form), spacegroup P22121
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
- 7SRV
- Type
- protein
- Length
- 3,082 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, CA, CO3, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 34% 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 | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 518 | 33% helix, 22% strand | Q8IL11 |
| C | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 524 | 33% helix, 22% strand | Q8IL11 |
| D | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 506 | 34% helix, 22% strand | Q8IL11 |
| E | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 513 | 34% helix, 22% strand | Q8IL11 |
| F | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 502 | 34% helix, 22% strand | Q8IL11 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, C, B, D, F, E
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, F
- GOL · Glycerol · additive · chains 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.82 | 0.83 | 103 | CO3, ACT |
| 2 | 758 | 0.81 | 0.84 | 76 | CO3, ACT, EDO |
| 3 | 798 | 0.81 | 0.84 | 77 | CO3, ACT |
| 4 | 864 | 0.80 | 0.82 | 77 | CO3, ACT |
| 5 | 584 | 0.79 | 0.85 | 72 | CO3, ACT |
Interfaces
13 interfaces between chains.
- A–C · 1496 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1486 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1481 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1343 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1217 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 7SRV · Metal dependent activation of Plasmodium falciparum M17 aminopeptidase (inactive form)… · 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 7SRV · PDBe 7SRV · UniProt Q8IL11
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