MolNFT v1 · #48566 · protein
Crystal structure of the murray valley encephalitis virus NS5 2'-O methyltransferase domain in complex with sah and 7M-GTP
2PX8 · Genome polyprotein [contains: capsid protein C (core…: “Crystal structure of the murray valley encephalitis virus NS5 2'-O methyltransferase domain in complex with…”. X-ray diffraction, 4 ligands (MGT, 3PO, SAH), 4 pockets (best…
- PDB
- 2PX8
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein [contains: capsid protein C (core protein)
- EC
- 2.7.7.48
- UniProt
- P05769
- Ligands
- MGT, 3PO, SAH, CL
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein [contains: capsid protein C (core protein) (EC 2.7.7.48) | protein | 264 | 36% helix, 15% strand | P05769 |
| B | Genome polyprotein [contains: capsid protein C (core protein) (EC 2.7.7.48) | protein | 265 | 35% helix, 16% strand | P05769 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 3 copies · chains A, B
- 3PO · Triphosphate · ligand · 2 copies · chains A, B
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.69 | 0.78 | 60 | MGT, 3PO, SAH |
| 2 | 511 | 0.66 | 0.78 | 55 | SAH |
| 3 | 235 | 0.49 | 0.75 | 33 | CL |
| 4 | 53 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 160 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (methylation).
Compared structures
- 2PX8 · Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase… · the same entry in another collection · chain B against B, 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 P05769
- Elsewhere: RCSB PDB 2PX8 · PDBe 2PX8 · UniProt P05769
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