Research workbench
Crystal structure of the human MTERF4:NSUN4:SAM ternary complex
Analyse Crystal structure of the human MTERF4:NSUN4:SAM ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FZV
- Type
- protein
- Length
- 575 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative methyltransferase NSUN4; Mterf domain-containing protein 2
- EC
- 2.1.1.-
- UniProt
- Q96CB9, Q7Z6M4
- Ligands
- SAM
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative methyltransferase NSUN4 (EC 2.1.1.-) | protein | 342 | 40% helix, 20% strand | Q96CB9 |
| B | Mterf domain-containing protein 2 | protein | 233 | 68% helix, 0% strand | Q7Z6M4 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- FMT · Formic acid · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.75 | 0.80 | 79 | empty |
| 2 | 559 | 0.67 | 0.77 | 57 | SAM |
| 3 | 73 | 0.41 | 0.80 | 13 | empty |
| 4 | 78 | 0.39 | 0.78 | 17 | empty |
| 5 | 58 | 0.35 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 4FZV · Crystal structure of the human MTERF4:NSUN4:SAM ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q96CB9 · AlphaFold monomer V2.0 prediction for 5-methylcytosine rRNA methyltransferase NSUN4… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q7Z6M4 · AlphaFold monomer V2.0 prediction for transcription termination factor 4, mitochondrial… · 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 Q96CB9
- Every structure of UniProt Q7Z6M4
- Elsewhere: RCSB PDB 4FZV · PDBe 4FZV · UniProt Q96CB9 · UniProt Q7Z6M4
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