MolNFT v1 · #145643 · protein
Crystal structure of a protein arginine N-methyltransferase from naegleria fowleri
6CU3: “Crystal structure of a protein arginine N-methyltransferase from naegleria fowleri”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #145643 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CU3
- Type
- protein
- Length
- 1,819 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein arginine N-methyltransferase | protein | 311 | 27% helix, 39% strand | — |
| B | Protein arginine N-methyltransferase | protein | 312 | 27% helix, 39% strand | — |
| C | Protein arginine N-methyltransferase | protein | 306 | 26% helix, 40% strand | — |
| E | Protein arginine N-methyltransferase | protein | 309 | 26% helix, 40% strand | — |
| F | Protein arginine N-methyltransferase | protein | 270 | 26% helix, 34% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, E, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.75 | 0.79 | 109 | empty |
| 2 | 333 | 0.65 | 0.80 | 43 | EDO |
| 3 | 366 | 0.63 | 0.78 | 36 | empty |
| 4 | 268 | 0.63 | 0.81 | 38 | empty |
| 5 | 315 | 0.63 | 0.79 | 44 | EDO |
Interfaces
6 interfaces between chains.
- B–E · 1463 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 1180 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 841 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 806 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 466 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (additive adduct, disulfide).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6CU3 · PDBe 6CU3
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