MolNFT v1 · #142291 · protein
Proteobacterial origin of protein arginine methylation and regulation of complex I assembly by mida
5ZZW · Protein arginine methyltransferase NDUFAF7 homolog…: “Proteobacterial origin of protein arginine methylation and regulation of complex I assembly by mida”. X-ray diffraction, 1 ligand (SAH), 7 pockets (best druggability 0.80).…
- PDB
- 5ZZW
- Type
- protein
- Length
- 1,200 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
- EC
- 2.1.1.320
- UniProt
- Q54S83
- Ligands
- SAH
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial (EC 2.1.1.320) | protein | 400 | 37% helix, 23% strand | Q54S83 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.80 | 0.81 | 105 | empty |
| 2 | 476 | 0.78 | 0.86 | 58 | SAH |
| 3 | 785 | 0.75 | 0.79 | 73 | SAH |
| 4 | 579 | 0.74 | 0.81 | 63 | SAH |
| 5 | 144 | 0.43 | 0.75 | 25 | empty |
Interfaces
2 interfaces between chains.
- B–A · 1087 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ZZW · Proteobacterial origin of protein arginine methylation and regulation of Complex I… · the same entry in another collection · chain B against B, TM-score 1.00
- Q54S83 · AlphaFold monomer V2.0 prediction for protein arginine methyltransferase NDUFAF7 homolog… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q54S83
- Elsewhere: RCSB PDB 5ZZW · PDBe 5ZZW · UniProt Q54S83
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.