Research workbench
M296I mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA
Analyse M296I mutant of foot-and-mouth disease virus RNA-polymerase 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
- 3KNA
- Type
- protein + RNA
- Length
- 488 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3D polymerase; RNA (5'-R(*AP*UP*GP*GP*GP*CP*C)-3'); RNA (5'-R(*GP*GP*CP*CP*C)-3')
- EC
- 2.7.7.48
- UniProt
- Q9QCE3
- Ligands
- MG
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3D polymerase (EC 2.7.7.48) | protein | 476 | 40% helix, 17% strand | Q9QCE3 |
| B | RNA (5'-R(*AP*UP*GP*GP*GP*CP*C)-3') | rna | 7 | — | — |
| C | RNA (5'-R(*GP*GP*CP*CP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 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 | 1044 | 0.78 | 0.80 | 80 | MG |
| 2 | 191 | 0.69 | 0.87 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 974 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 606 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 257 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Compared structures
- 3KNA · M296I mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template… · 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 Q9QCE3
- Elsewhere: RCSB PDB 3KNA · PDBe 3KNA · UniProt Q9QCE3
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