MolNFT v1 · #168943 · protein
Plasmodium vivax M17 leucyl aminopeptidase
6WVV: “Plasmodium vivax M17 leucyl aminopeptidase”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.84). MolNFT v1 #168943 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WVV
- Type
- protein
- Length
- 5,793 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M17 leucyl aminopeptidase
- EC
- 3.4.11.1
- UniProt
- A0A1G4HHP8
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 12 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 509 | 35% helix, 21% strand | A0A1G4HHP8 |
| B | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 508 | 35% helix, 21% strand | A0A1G4HHP8 |
| C | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 507 | 36% helix, 21% strand | A0A1G4HHP8 |
| D | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 507 | 36% helix, 21% strand | A0A1G4HHP8 |
| E | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 503 | 33% helix, 20% strand | A0A1G4HHP8 |
| F | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 497 | 33% helix, 19% strand | A0A1G4HHP8 |
| G | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 466 | 35% helix, 20% strand | A0A1G4HHP8 |
| H | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 478 | 36% helix, 20% strand | A0A1G4HHP8 |
| I | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 467 | 36% helix, 21% strand | A0A1G4HHP8 |
| J | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 458 | 36% helix, 19% strand | A0A1G4HHP8 |
| K | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 440 | 37% helix, 19% strand | A0A1G4HHP8 |
| L | M17 leucyl aminopeptidase (EC 3.4.11.1) | protein | 453 | 35% helix, 20% strand | A0A1G4HHP8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 18 copies · chains A, C, F, B, D, E, G, I, J, H, K, L
- GOL · Glycerol · additive · 30 copies · chains A, E, C, F, B, D, G, I, H, L, J, K
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C, D, E, F, G, 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 | 1187 | 0.84 | 0.85 | 126 | empty |
| 2 | 509 | 0.81 | 0.87 | 68 | empty |
| 3 | 428 | 0.80 | 0.88 | 67 | empty |
| 4 | 340 | 0.78 | 0.88 | 55 | empty |
| 5 | 831 | 0.77 | 0.81 | 87 | GOL, PEG |
Interfaces
25 interfaces between chains.
- B–E · 1446 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1444 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1440 Ų buried · 22 hydrogen bonds · protein-protein
- G–I · 1433 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1430 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6WVV · Plasmodium vivax M17 leucyl aminopeptidase · the same entry in another collection · chain K against K, 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 A0A1G4HHP8
- Elsewhere: RCSB PDB 6WVV · PDBe 6WVV · UniProt A0A1G4HHP8
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