MolNFT v1 · #35385 · protein + RNA
Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin
2E9R · 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3': “Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with…”. X-ray diffraction, 2 ligands (RTP, MG), 4 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2E9R
- Type
- protein + RNA
- Length
- 491 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'; 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3'; RNA-dependent…
- EC
- 2.7.7.48
- UniProt
- Q0QEE1
- Ligands
- RTP, MG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3' | rna | 9 | — | — |
| B | 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3' | rna | 6 | — | — |
| X | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 476 | 41% helix, 15% strand | Q0QEE1 |
Ligands and binding sites
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 | 944 | 0.80 | 0.82 | 63 | RTP |
| 2 | 146 | 0.66 | 0.87 | 26 | empty |
| 3 | 53 | 0.46 | 0.85 | 15 | empty |
| 4 | 56 | 0.24 | 0.72 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–X · 1126 Ų buried · 39 hydrogen bonds · protein-nucleic
- B–X · 656 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–B · 319 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 2E9R · Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a… · 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 Q0QEE1
- Elsewhere: RCSB PDB 2E9R · PDBe 2E9R · UniProt Q0QEE1
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