Research workbench
Mutant M16A of RNA dependent RNA polymerase 3D from foot-and-mouth disease virus complexed with an template -primer RNA
Analyse Mutant M16A of RNA dependent RNA polymerase 3D from foot-and-mouth disease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GVY
- Type
- protein + RNA
- Length
- 487 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; RNA (5'-R(P*CP*CP*GP*GP*G)-3'); RNA…
- UniProt
- Q0QEE0
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 475 | 41% helix, 18% strand | Q0QEE0 |
| B | RNA (5'-R(P*CP*CP*GP*GP*G)-3') | rna | 5 | — | — |
| C | RNA (5'-R(P*CP*UP*CP*CP*CP*GP*GP*G)-3') | rna | 7 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains 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 | 1087 | 0.80 | 0.82 | 77 | empty |
| 2 | 134 | 0.62 | 0.86 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 861 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 652 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 297 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 6GVY · Mutant M16A of RNA dependent RNA polymerase 3D from Foot-and-Mouth disease Virus… · 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 Q0QEE0
- Elsewhere: RCSB PDB 6GVY · PDBe 6GVY · UniProt Q0QEE0
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