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Crystal structure of SARS-cov-2 nucleocapsid protein C-terminal RNA binding domain at 2.0A resolution

Analyse Crystal structure of SARS-cov-2 nucleocapsid protein C-terminal RNA binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F2B
Type: protein
Length: 212 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Ligands: PO4, CL
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Nucleoprotein	protein	106	41% helix, 21% strand	P0DTC9

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains B, A
CL · Chloride ion · ion · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	97	0.43	0.78	21	empty
2	76	0.34	0.75	22	empty

Interfaces

1 interface between chains.

B–A · 2574 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

7F2B · Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain at… · the same entry in another collection · chain B against B, 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 P0DTC9
Elsewhere: RCSB PDB 7F2B · PDBe 7F2B · UniProt P0DTC9

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