Research workbench
Proteobacterial origin of protein arginine methylation and regulation of complex I assembly by mida
Analyse Proteobacterial origin of protein arginine methylation and regulation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZU0
- 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
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, 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 A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 924 | 0.79 | 0.81 | 81 | SAH |
| 2 | 1167 | 0.77 | 0.79 | 100 | SAH |
| 3 | 583 | 0.77 | 0.83 | 56 | SAH |
| 4 | 54 | 0.71 | 0.98 | 17 | empty |
| 5 | 234 | 0.60 | 0.80 | 38 | empty |
Interfaces
2 interfaces between chains.
- A–C · 883 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 689 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 5ZU0 · 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 B against A, TM-score 0.98
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 5ZU0 · PDBe 5ZU0 · UniProt Q54S83
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