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A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases
Analyse A bestatin-based chemical biology strategy reveals distinct roles for malaria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T8W
- Type
- protein
- Length
- 6,173 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 leucyl aminopeptidase
- UniProt
- Q8IL11
- Ligands
- DGZ, ZN, SO4, CO3
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M17 leucyl aminopeptidase | protein | 519 | 35% helix, 22% strand | Q8IL11 |
| B | M17 leucyl aminopeptidase | protein | 517 | 35% helix, 22% strand | Q8IL11 |
| C | M17 leucyl aminopeptidase | protein | 516 | 36% helix, 22% strand | Q8IL11 |
| D, J | M17 leucyl aminopeptidase | protein | 514 | 36% helix, 22% strand | Q8IL11 |
| E, K | M17 leucyl aminopeptidase | protein | 509 | 35% helix, 22% strand | Q8IL11 |
| F, L | M17 leucyl aminopeptidase | protein | 511 | 36% helix, 22% strand | Q8IL11 |
| G | M17 leucyl aminopeptidase | protein | 517 | 36% helix, 22% strand | Q8IL11 |
| H, I | M17 leucyl aminopeptidase | protein | 518 | 35% helix, 22% strand | Q8IL11 |
Ligands and binding sites
- DGZ · N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide · ligand · 12 copies · chains A, B, F, E, C, D, G, H, L, K, I, J
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 29 copies · chains A, D, B, C, E, F, G, J, I, H, K, L
- CO3 · Carbonate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 1PE · Pentaethylene glycol · additive · 33 copies · chains A, C, D, E, F, G, I, J, K, L
- 2PE · Nonaethylene glycol · additive · 2 copies · chains B, H
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 | 903 | 0.76 | 0.79 | 61 | SO4 |
| 2 | 828 | 0.74 | 0.79 | 70 | CO3, DGZ |
| 3 | 821 | 0.74 | 0.78 | 68 | CO3, DGZ |
| 4 | 839 | 0.73 | 0.78 | 66 | DGZ |
| 5 | 807 | 0.73 | 0.78 | 67 | CO3, DGZ |
Interfaces
26 interfaces between chains.
- H–I · 1512 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1506 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1503 Ų buried · 26 hydrogen bonds · protein-protein
- G–I · 1496 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1495 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3T8W · A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and… · 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 3T8W · PDBe 3T8W · UniProt Q8IL11
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