Research workbench
Crystal structure of the heterodimeric vaccinia virus polyadenylate polymerase with bound ATP-gamma-S
Analyse Crystal structure of the heterodimeric vaccinia virus polyadenylate polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GA9
- Type
- protein
- Length
- 733 residues
- Chains
- 2
- 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
- AGS, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 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 | 39% helix, 18% strand | P07617 |
| D | POLY(A) polymerase catalytic subunit (EC 2.7.7.19) | protein | 445 | 49% helix, 16% strand | P23371 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 2 copies · chains D
- CA · Calcium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 678 | 0.78 | 0.83 | 65 | CA, AGS |
| 2 | 260 | 0.63 | 0.81 | 33 | empty |
| 3 | 288 | 0.59 | 0.78 | 38 | empty |
| 4 | 235 | 0.56 | 0.78 | 35 | empty |
| 5 | 204 | 0.52 | 0.77 | 36 | empty |
Interfaces
1 interface between chains.
- A–D · 1843 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 2GA9 · Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound… · 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 2GA9 · PDBe 2GA9 · UniProt P07617 · UniProt P23371
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