Research workbench
Foot and mouth disease virus RNA-dependent RNA polymerase in complex with uridylylated vpg protein
Analyse Foot and mouth disease virus RNA-dependent RNA polymerase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F8E
- Type
- protein
- Length
- 489 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-dpendent RNA polymerase; Vpg protein
- EC
- 2.7.7.48
- Ligands
- U5P, MN, MG
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | RNA-dpendent RNA polymerase (EC 2.7.7.48) | protein | 474 | 39% helix, 18% strand | — |
| A | Vpg protein | protein | 15 | 0% helix, 0% strand | — |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · chains X, A
- MN · Manganese (II) ion · metal · chains X, A
- MG · Magnesium ion · metal · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.81 | 0.83 | 89 | MN, MG, U5P |
| 2 | 375 | 0.68 | 0.81 | 43 | empty |
Interfaces
1 interface between chains.
- X–A · 1092 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2F8E · Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated… · the same entry in another collection · chain X against X, 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
- Elsewhere: RCSB PDB 2F8E · PDBe 2F8E
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