MolNFT v1 · #169066 · protein

Structure of SARS-cov-2 nucleocapsid dimerization domain, P1 form

6WZO · Nucleoprotein: “Structure of SARS-cov-2 nucleocapsid dimerization domain, P1 form”. X-ray diffraction, 5 pockets (best druggability 0.46). MolNFT v1 #169066 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WZO
Type: protein
Length: 437 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Pockets: 5 · best druggability 0.46

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Nucleoprotein	protein	108	41% helix, 20% strand	P0DTC9
B	Nucleoprotein	protein	111	40% helix, 18% strand	P0DTC9
D	Nucleoprotein	protein	110	40% helix, 20% strand	P0DTC9

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	223	0.46	0.73	32	empty
2	119	0.42	0.76	16	empty
3	66	0.31	0.75	15	empty
4	58	0.28	0.74	14	empty
5	56	0.27	0.74	17	empty

Interfaces

3 interfaces between chains.

C–D · 2697 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 2684 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 220 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6WZO · Structure of SARS-CoV-2 Nucleocapsid dimerization domain, P1 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 6WZO · PDBe 6WZO · UniProt P0DTC9

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