MolNFT v1 · #149007 · protein
Crystal structure of toxoplasma gondii akmt
6FND · Apical complex lysine methyltransferase: “Crystal structure of toxoplasma gondii akmt”. X-ray diffraction, 2 ligands (ZN, SO4), 20 pockets (best druggability 0.85). MolNFT v1 #149007 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6FND
- Type
- protein
- Length
- 1,683 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apical complex lysine methyltransferase
- UniProt
- A0A151H4R7
- Ligands
- ZN, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apical complex lysine methyltransferase | protein | 423 | 48% helix, 14% strand | A0A151H4R7 |
| B | Apical complex lysine methyltransferase | protein | 418 | 50% helix, 14% strand | A0A151H4R7 |
| C | Apical complex lysine methyltransferase | protein | 420 | 50% helix, 13% strand | A0A151H4R7 |
| D | Apical complex lysine methyltransferase | protein | 422 | 50% helix, 14% strand | A0A151H4R7 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.85 | 0.87 | 92 | SO4, GOL, EDO |
| 2 | 1195 | 0.82 | 0.83 | 132 | GOL, EDO, SO4 |
| 3 | 918 | 0.75 | 0.78 | 65 | empty |
| 4 | 783 | 0.73 | 0.78 | 62 | empty |
| 5 | 54 | 0.70 | 0.97 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2048 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2002 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1907 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1800 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 modified (methylation).
Compared structures
- 6FND · Crystal structure of Toxoplasma gondii AKMT · 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 A0A151H4R7
- Elsewhere: RCSB PDB 6FND · PDBe 6FND · UniProt A0A151H4R7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.