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2.05 ångström resolution crystal structure of C-terminal dimerization domain of nucleocapsid phosphoprotein from SARS-cov-2

Analyse 2.05 ångström resolution crystal structure of C-terminal dimerization domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WJI
Type: protein
Length: 648 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Ligands: CL
Pockets: 5 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Nucleoprotein	protein	108	40% helix, 19% strand	P0DTC9

Ligands and binding sites

CL · Chloride ion · ion · 9 copies · chains A, B, C, D, E, F

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

Pockets

5 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	262	0.49	0.74	31	CL
2	234	0.48	0.74	29	CL
3	154	0.44	0.75	24	empty
4	63	0.30	0.74	11	empty
5	51	0.29	0.75	15	empty

Interfaces

7 interfaces between chains.

C–D · 2727 Å² buried · 41 hydrogen bonds · protein-protein
E–F · 2721 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 2719 Å² buried · 39 hydrogen bonds · protein-protein
B–E · 313 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 144 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6WJI · 2.05 Angstrom Resolution Crystal Structure of C-terminal Dimerization Domain of… · 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 6WJI · PDBe 6WJI · UniProt P0DTC9

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