MolNFT v1 · #47414 · protein
Crystal structure of meaban virus nucleoside-2'-O- methyltransferase
2OXT · Nucleoside-2'-O-methyltransferase: “Crystal structure of meaban virus nucleoside-2'-O- methyltransferase”. X-ray diffraction, 1 ligand (SAM), 11 pockets (best druggability 0.81). MolNFT v1 #47414 on GenesisL1: 3D structure, binding…
- PDB
- 2OXT
- Type
- protein
- Length
- 1,060 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside-2'-O-methyltransferase
- UniProt
- A0EKU1
- Ligands
- SAM
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Nucleoside-2'-O-methyltransferase | protein | 265 | 39% helix, 17% strand | A0EKU1 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.81 | 0.82 | 118 | SAM |
| 2 | 640 | 0.79 | 0.84 | 62 | SAM |
| 3 | 563 | 0.78 | 0.85 | 66 | SAM |
| 4 | 542 | 0.64 | 0.76 | 60 | empty |
| 5 | 184 | 0.45 | 0.74 | 31 | empty |
Interfaces
3 interfaces between chains.
- C–D · 986 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2OXT · Crystal structure of Meaban virus nucleoside-2'-O-methyltransferase · the same entry in another collection · chain A 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 A0EKU1
- Elsewhere: RCSB PDB 2OXT · PDBe 2OXT · UniProt A0EKU1
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