MolNFT v1 · #123867 · protein + RNA
Mutant GC216/7AA of 3D polymerase from foot-and-mouth disease virus
5JXS · RNA dependent RNA polymerase: “Mutant GC216/7AA of 3D polymerase from foot-and-mouth disease virus”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.80). MolNFT v1 #123867 on GenesisL1: 3D structure, binding sites…
- PDB
- 5JXS
- Type
- protein + RNA
- Length
- 490 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase; RNA template; RNA primer
- EC
- 2.7.7.48
- UniProt
- P03311
- Ligands
- MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase (EC 2.7.7.48) | protein | 476 | 41% helix, 17% strand | P03311 |
| B | RNA template | rna | 8 | — | — |
| C | RNA primer | rna | 6 | — | — |
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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.80 | 0.82 | 89 | MG |
| 2 | 176 | 0.65 | 0.85 | 27 | empty |
| 3 | 54 | 0.44 | 0.84 | 15 | empty |
| 4 | 70 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 941 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 660 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 281 Ų buried · 27 hydrogen bonds · nucleic-nucleic
Compared structures
- 5JXS · Mutant GC216/7AA of 3D polymerase 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 P03311
- Elsewhere: RCSB PDB 5JXS · PDBe 5JXS · UniProt P03311
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