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Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with uu and 3'-deoxy ATP
Analyse Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ER9
- Type
- protein + RNA
- Length
- 735 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase; POLY(A) polymerase catalytic…
- EC
- 2.1.1.57, 2.7.7.19
- UniProt
- P07617, P23371
- Ligands
- 3AT, CA
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (EC 2.1.1.57) | protein | 288 | 40% helix, 17% strand | P07617 |
| B | POLY(A) polymerase catalytic subunit (EC 2.7.7.19) | protein | 445 | 49% helix, 16% strand | P23371 |
| D | 5'-R(UP*U)-3' | rna | 2 | — | — |
Ligands and binding sites
- 3AT · 3'-deoxyadenosine-5'-triphosphate · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.77 | 0.83 | 62 | 3AT, CA |
| 2 | 228 | 0.61 | 0.81 | 34 | empty |
| 3 | 286 | 0.59 | 0.79 | 40 | empty |
| 4 | 233 | 0.55 | 0.78 | 39 | empty |
| 5 | 172 | 0.55 | 0.80 | 33 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1801 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 307 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3ER9 · Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase… · 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 P07617
- Every structure of UniProt P23371
- Elsewhere: RCSB PDB 3ER9 · PDBe 3ER9 · UniProt P07617 · UniProt P23371
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