MolNFT v1 · #184319 · protein
Thosea asigna virus rdrp domain in complex with MG+2
7OM2 · RNA-dependent RNA polymerase: “Thosea asigna virus rdrp domain in complex with MG+2”. X-ray diffraction, 2 ligands (MG, SO4), 19 pockets (best druggability 0.73). MolNFT v1 #184319 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7OM2
- Type
- protein
- Length
- 1,320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dependent RNA polymerase
- UniProt
- Q6A562
- Ligands
- MG, SO4
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-dependent RNA polymerase | protein | 659 | 45% helix, 13% strand | Q6A562 |
| B | RNA-dependent RNA polymerase | protein | 661 | 45% helix, 14% strand | Q6A562 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.73 | 0.77 | 80 | SO4 |
| 2 | 280 | 0.65 | 0.81 | 40 | SO4 |
| 3 | 97 | 0.58 | 0.86 | 20 | empty |
| 4 | 199 | 0.57 | 0.80 | 29 | SO4 |
| 5 | 194 | 0.54 | 0.78 | 29 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2936 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 7OM2 · Thosea asigna virus RdRP domain in complex with Mg+2 · 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 Q6A562
- Elsewhere: RCSB PDB 7OM2 · PDBe 7OM2 · UniProt Q6A562
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