MolNFT v1 · #91194 · protein
Location of the dsrna-dependent polymerase, VP1, in rotavirus particles
4F5X · VP2 protein: “Location of the dsrna-dependent polymerase, VP1, in rotavirus particles”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #91194 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4F5X
- Type
- protein
- Length
- 7,727 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP2 protein; Intermediate capsid protein VP6; RNA-directed RNA polymerase
- EC
- 2.7.7.48
- UniProt
- H9N1A6, A7J3A1, O37061
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP2 protein | protein | 781 | 41% helix, 9% strand | H9N1A6 |
| B | VP2 protein | protein | 810 | 41% helix, 9% strand | H9N1A6 |
| C, D, E, F, G, H, I, J, K, L, M, N, O | Intermediate capsid protein VP6 | protein | 397 | 29% helix, 32% strand | A7J3A1 |
| W | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 975 | 49% helix, 8% strand | O37061 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains C, D, E, F, G, H, I, J, K, L, M, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.87 | 0.94 | 90 | empty |
| 2 | 863 | 0.87 | 0.90 | 120 | empty |
| 3 | 782 | 0.87 | 0.90 | 114 | empty |
| 4 | 514 | 0.86 | 0.93 | 82 | empty |
| 5 | 515 | 0.86 | 0.93 | 87 | empty |
Interfaces
41 interfaces between chains.
- I–K · 2630 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2621 Ų buried · 37 hydrogen bonds · protein-protein
- L–M · 2609 Ų buried · 42 hydrogen bonds · protein-protein
- D–E · 2609 Ų buried · 37 hydrogen bonds · protein-protein
- L–N · 2603 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4F5X · Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles · 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 H9N1A6
- Every structure of UniProt A7J3A1
- Every structure of UniProt O37061
- Elsewhere: RCSB PDB 4F5X · PDBe 4F5X · UniProt H9N1A6 · UniProt A7J3A1 · UniProt O37061
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