MolNFT v1 · #91842 · protein
Human MTERF4-NSUN4 protein complex
4FP9 · Methyltransferase NSUN4: “Human MTERF4-NSUN4 protein complex”. X-ray diffraction, 2 ligands (SAM, SO4), 20 pockets (best druggability 0.74). MolNFT v1 #91842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4FP9
- Type
- protein
- Length
- 2,327 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase NSUN4; Mterf domain-containing protein 2
- EC
- 2.1.1.-
- UniProt
- Q96CB9, Q7Z6M4
- Ligands
- SAM, SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F | Methyltransferase NSUN4 (EC 2.1.1.-) | protein | 338 | 41% helix, 20% strand | Q96CB9 |
| B, E, G, H | Mterf domain-containing protein 2 | protein | 245 | 71% helix, 0% strand | Q7Z6M4 |
| D | Methyltransferase NSUN4 (EC 2.1.1.-) | protein | 333 | 41% helix, 20% strand | Q96CB9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, C, D, F
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D, G, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.74 | 0.77 | 79 | empty |
| 2 | 555 | 0.72 | 0.80 | 49 | SAM |
| 3 | 661 | 0.71 | 0.78 | 54 | SAM, SO4 |
| 4 | 668 | 0.71 | 0.78 | 54 | SAM |
| 5 | 665 | 0.71 | 0.78 | 52 | SAM |
Interfaces
11 interfaces between chains.
- C–E · 775 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 771 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 768 Ų buried · 14 hydrogen bonds · protein-protein
- F–H · 767 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 657 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4FP9 · Human MTERF4-NSUN4 protein complex · the same entry in another collection · chain C against C, TM-score 1.00
- Q7Z6M4 · AlphaFold monomer V2.0 prediction for transcription termination factor 4, mitochondrial… · a predicted model of the same protein · chain E 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 F against A, TM-score 1.00
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 4FP9 · PDBe 4FP9 · UniProt Q96CB9 · UniProt Q7Z6M4
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