Research workbench
Crystal structure of the methyltransferase subunit of human mitochondrial ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)
Analyse Crystal structure of the methyltransferase subunit of human mitochondrial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFJ
- Type
- protein
- Length
- 533 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial ribonuclease P protein 1
- EC
- 2.1.1.-
- UniProt
- Q7L0Y3
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mitochondrial ribonuclease P protein 1 (EC 2.1.1.-) | protein | 178 | 42% helix, 14% strand | Q7L0Y3 |
| B | Mitochondrial ribonuclease P protein 1 (EC 2.1.1.-) | protein | 177 | 44% helix, 15% strand | Q7L0Y3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.79 | 0.81 | 99 | GOL, SAM |
| 2 | 215 | 0.74 | 0.89 | 34 | SAM |
| 3 | 209 | 0.74 | 0.89 | 35 | SAM |
| 4 | 262 | 0.57 | 0.78 | 28 | EDO |
| 5 | 181 | 0.54 | 0.79 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 678 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5NFJ · Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P… · the same entry in another collection · chain C against C, TM-score 1.00
- Q7L0Y3 · AlphaFold monomer V2.0 prediction for tRNA methyltransferase 10 homolog C (Q7L0Y3) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q7L0Y3
- Elsewhere: RCSB PDB 5NFJ · PDBe 5NFJ · UniProt Q7L0Y3
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