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Location of the dsrna-dependent polymerase, VP1, in rotavirus particles

Analyse Location of the dsrna-dependent polymerase, VP1, in rotavirus particles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 39 hydrogen bonds · protein-protein
G–H · 2621 Å² buried · 37 hydrogen bonds · protein-protein
L–M · 2609 Å² buried · 42 hydrogen bonds · protein-protein
D–E · 2609 Å² buried · 37 hydrogen bonds · protein-protein
L–N · 2603 Å² 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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