MolNFT v1 · #35393 · protein + RNA
Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP and UTP
2E9Z · 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3': “Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP and UTP”. X-ray diffraction, 3 ligands (UTP, PPV, MG), 5 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2E9Z
- Type
- protein + RNA
- Length
- 492 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(*GP*GP*GP*CP*CP*CP*A)-3'; RNA-dependent RNA…
- EC
- 2.7.7.48
- UniProt
- Q0QEE1
- Ligands
- UTP, PPV, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3' | rna | 9 | — | — |
| C | 5'-R(*GP*GP*GP*CP*CP*CP*A)-3' | rna | 7 | — | — |
| A | RNA-dependent RNA polymerase (EC 2.7.7.48) | protein | 476 | 40% helix, 14% strand | Q0QEE1 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · chains B, C, A
- PPV · Pyrophosphate · ligand · chains C, A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.80 | 0.82 | 69 | MG, UTP, PPV |
| 2 | 126 | 0.63 | 0.88 | 24 | empty |
| 3 | 124 | 0.43 | 0.77 | 26 | empty |
| 4 | 53 | 0.30 | 0.76 | 17 | empty |
| 5 | 53 | 0.29 | 0.76 | 16 | MG |
Interfaces
3 interfaces between chains.
- B–A · 1018 Ų buried · 22 hydrogen bonds · protein-nucleic
- C–A · 699 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 336 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 2E9Z · Foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA, ATP… · 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 2E9Z · PDBe 2E9Z · UniProt Q0QEE1
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