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Structure of SARS-cov-2 nucleocapsid dimerization domain, P21 form

Analyse Structure of SARS-cov-2 nucleocapsid dimerization domain, P21 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZQ
Type: protein
Length: 459 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Ligands: SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nucleoprotein	protein	114	43% helix, 19% strand	P0DTC9
C	Nucleoprotein	protein	116	42% helix, 17% strand	P0DTC9
D	Nucleoprotein	protein	115	43% helix, 17% strand	P0DTC9

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.72	0.75	89	SO4
2	82	0.35	0.75	24	empty
3	58	0.29	0.74	14	empty

Interfaces

5 interfaces between chains.

C–D · 2724 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2674 Å² buried · 44 hydrogen bonds · protein-protein
A–D · 301 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 91 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 52 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6WZQ · Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P21 form · 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 P0DTC9
Elsewhere: RCSB PDB 6WZQ · PDBe 6WZQ · UniProt P0DTC9

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