MolNFT v1 · #91762 · protein
Crystal structure of methyltransferase domain of human RNA (guanine-9- ) methyltransferase domain containing protein 2
4FMW · RNA (guanine-9-)-methyltransferase domain-containing…: “Crystal structure of methyltransferase domain of human RNA (guanine-9- ) methyltransferase domain containing…”. X-ray diffraction, 3 ligands (SAH, K, UNX), 4 pockets (best…
- PDB
- 4FMW
- Type
- protein
- Length
- 350 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (guanine-9-)-methyltransferase domain-containing protein 2
- EC
- 2.1.1.-
- UniProt
- Q8TBZ6
- Ligands
- SAH, K, UNX
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (guanine-9-)-methyltransferase domain-containing protein 2 (EC 2.1.1.-) | protein | 178 | 42% helix, 15% strand | Q8TBZ6 |
| B | RNA (guanine-9-)-methyltransferase domain-containing protein 2 (EC 2.1.1.-) | protein | 172 | 43% helix, 16% strand | Q8TBZ6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- UNX · Unknown atom or ion · ion · 20 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.72 | 0.88 | 30 | SAH, UNX |
| 2 | 206 | 0.72 | 0.88 | 29 | SAH |
| 3 | 384 | 0.59 | 0.76 | 52 | UNX |
| 4 | 56 | 0.43 | 0.83 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 4FMW · Crystal structure of methyltransferase domain of human RNA (guanine-9-) methyltransferase… · the same entry in another collection · chain B against B, TM-score 1.00
- Q8TBZ6 · AlphaFold monomer V2.0 prediction for tRNA methyltransferase 10 homolog a (Q8TBZ6) · a predicted model of the same protein · chain B 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 Q8TBZ6
- Elsewhere: RCSB PDB 4FMW · PDBe 4FMW · UniProt Q8TBZ6
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