MolNFT v1 · #59971 · protein
Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3DPOL) in complex with protein primer vpg and a pyrophosphate
3CDW · RNA-directed RNA polymerase 3D-pol: “Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3DPOL) in complex with protein primer…”. X-ray diffraction, 2 ligands (POP, CL), 4 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3CDW
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase 3D-pol; Protein 3B
- EC
- 2.7.7.48
- UniProt
- P03313
- Ligands
- POP, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 40% 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 |
| H | Protein 3B | protein | 9 | 0% helix, 22% strand | P03313 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- CL · Chloride ion · ion · 7 copies · chains A
- GOL · Glycerol · additive · 27 copies · chains A, H
- ACT · Acetate ion · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.72 | 0.77 | 86 | CL, POP, GOL |
| 2 | 420 | 0.61 | 0.76 | 46 | CL, GOL |
| 3 | 72 | 0.36 | 0.77 | 17 | GOL |
| 4 | 75 | 0.35 | 0.76 | 15 | CL |
Interfaces
1 interface between chains.
- A–H · 477 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3CDW · 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 3CDW · PDBe 3CDW · UniProt P03313
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