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Crystal structure of rift valley fever virus nucleocapsid protein tetramer bound to single-stranded RNA

Analyse Crystal structure of rift valley fever virus nucleocapsid protein tetramer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4H5P
Type: protein + RNA
Length: 1,004 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleocapsid protein; 28-mer POLY(U) RNA
UniProt: D3K5I7
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nucleocapsid protein	protein	244	68% helix, 1% strand	D3K5I7
E, F	28-mer POLY(U) RNA	rna	14	—	—

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.62	0.93	14	empty
2	162	0.59	0.83	26	empty
3	61	0.38	0.79	25	empty
4	126	0.37	0.74	14	empty
5	87	0.36	0.76	19	empty

Interfaces

6 interfaces between chains.

A–B · 1643 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1638 Å² buried · 18 hydrogen bonds · protein-protein
D–F · 1205 Å² buried · 28 hydrogen bonds · protein-nucleic
A–E · 1192 Å² buried · 29 hydrogen bonds · protein-nucleic
C–F · 1130 Å² buried · 28 hydrogen bonds · protein-nucleic

Compared structures

4H5P · Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Tetramer Bound to… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt D3K5I7
Elsewhere: RCSB PDB 4H5P · PDBe 4H5P · UniProt D3K5I7

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