Research workbench
Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a template-primer RNA and 5F-UTP
Analyse Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E9T
- Type
- protein + RNA
- Length
- 978 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3'; 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3'; RNA-dependent RNA…
- EC
- 2.7.7.48
- UniProt
- Q0QEE1
- Ligands
- PPV, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | 5'-R(P*UP*AP*GP*GP*GP*CP*CP*C)-3' | rna | 8 | — | — |
| C, F | 5'-R(*GP*GP*GP*CP*CP*CP*(5FU))-3' | rna | 7 | — | — |
| A, D | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 474 | 42% helix, 19% strand | Q0QEE1 |
Ligands and binding sites
- PPV · Pyrophosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.80 | 0.82 | 86 | MG, PPV |
| 2 | 1177 | 0.79 | 0.81 | 93 | MG, PPV |
| 3 | 113 | 0.70 | 0.92 | 34 | empty |
| 4 | 62 | 0.68 | 0.96 | 17 | empty |
| 5 | 493 | 0.64 | 0.76 | 43 | empty |
Interfaces
7 interfaces between chains.
- E–D · 896 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–A · 887 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–A · 663 Ų buried · 12 hydrogen bonds · protein-nucleic
- F–D · 658 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–D · 449 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 2E9T · Foot-and-mouth disease virus RNA-polymerase RNA dependent in complex with a… · 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 Q0QEE1
- Elsewhere: RCSB PDB 2E9T · PDBe 2E9T · UniProt Q0QEE1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.