Research workbench
Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA 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
- 3ERC
- Type
- protein + DNA + RNA
- Length
- 1,485 residues
- Chains
- 8
- 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
- U, 3AT, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cap-specific mRNA (nucleoside-2'-O-)-methyltransferase (EC 2.1.1.57) | protein | 288 | 38% helix, 17% strand | P07617 |
| C, D | POLY(A) polymerase catalytic subunit (EC 2.7.7.19) | protein | 445 | 48% helix, 13% strand | P23371 |
| E, F | RNA/DNA chimera (5'-D(CP*)R(UP*UP*)D(CP*C)-3') | dna | 5 | — | — |
| G | RNA/DNA chimera (5'-D(CP*)R(UP*UP*)-D(C)-3') | rna | 4 | — | — |
| I | RNA/DNA chimera (5'-D(CP*CP*)R(UP*UP*)D(C)-3') | dna | 5 | — | — |
Ligands and binding sites
- U · Uridine-5'-monophosphate · ligand · 2 copies · chains B, C, A, D
- 3AT · 3'-deoxyadenosine-5'-triphosphate · ligand · 2 copies · chains C, F, D, E
- CA · Calcium ion · metal · 4 copies · chains C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.85 | 0.92 | 81 | 3AT, CA |
| 2 | 584 | 0.81 | 0.86 | 82 | 3AT, CA |
| 3 | 791 | 0.73 | 0.78 | 91 | empty |
| 4 | 411 | 0.71 | 0.82 | 45 | empty |
| 5 | 272 | 0.69 | 0.85 | 41 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1843 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1811 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 737 Ų buried · 14 hydrogen bonds · protein-protein
- D–I · 605 Ų buried · 19 hydrogen bonds · protein-nucleic
- D–E · 482 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3ERC · Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with… · 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 3ERC · PDBe 3ERC · UniProt P07617 · UniProt P23371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.