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Crystal structure of SARS-cov-2 nucleocapsid protein N-terminal RNA binding domain

Analyse Crystal structure of SARS-cov-2 nucleocapsid protein N-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: 6M3M
Type: protein
Length: 499 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 2% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nucleoprotein	protein	121	2% helix, 26% strand	P0DTC9
B	Nucleoprotein	protein	126	2% helix, 23% strand	P0DTC9
C	Nucleoprotein	protein	126	2% helix, 22% strand	P0DTC9
D	Nucleoprotein	protein	126	2% helix, 26% strand	P0DTC9

Pockets

3 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	579	0.79	0.85	69	empty
2	189	0.62	0.83	31	empty
3	87	0.49	0.82	14	empty

Interfaces

5 interfaces between chains.

A–D · 337 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 326 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 296 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 208 Å² buried · 1 hydrogen bond · protein-protein
B–D · 159 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6M3M · Crystal structure of SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain · 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 P0DTC9
Elsewhere: RCSB PDB 6M3M · PDBe 6M3M · UniProt P0DTC9

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