MolNFT v1 · #59969 · protein
Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3DPOL) in complex with a pyrophosphate
3CDU · RNA-directed RNA polymerase 3D-pol: “Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3DPOL) in complex with a pyrophosphate”. X-ray diffraction, 3 ligands (POP, CL, SO4), 3 pockets (best druggability 0.73).…
- PDB
- 3CDU
- Type
- protein
- Length
- 468 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase 3D-pol
- EC
- 2.7.7.48
- UniProt
- P03313
- Ligands
- POP, CL, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase 3D-pol (EC 2.7.7.48) | protein | 468 | 41% helix, 15% strand | P03313 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- CL · Chloride ion · ion · 6 copies · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 30 copies · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.73 | 0.77 | 87 | CL, POP, GOL |
| 2 | 389 | 0.60 | 0.76 | 46 | CL, GOL |
| 3 | 66 | 0.34 | 0.76 | 13 | CL |
Compared structures
- 3CDU · Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex… · 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 P03313
- Elsewhere: RCSB PDB 3CDU · PDBe 3CDU · UniProt P03313
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