MolNFT v1 · #178033 · protein

SARS-cov-2 nucleocapsid protein C-terminal domain (dodecamer)

7F2E · Nucleoprotein: “SARS-cov-2 nucleocapsid protein C-terminal domain (dodecamer)”. X-ray diffraction, 1 ligand (PO4), 12 pockets (best druggability 0.75). MolNFT v1 #178033 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7F2E
Type: protein
Length: 1,233 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P0DTC9
Ligands: PO4
Pockets: 12 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 33% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, H, J	Nucleoprotein	protein	106	41% helix, 16% strand	P0DTC9
C, D, G, I	Nucleoprotein	protein	107	36% helix, 19% strand	P0DTC9
E, K	Nucleoprotein	protein	96	28% helix, 15% strand	P0DTC9
F	Nucleoprotein	protein	97	32% helix, 12% strand	P0DTC9
L	Nucleoprotein	protein	92	28% helix, 14% strand	P0DTC9

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains G, H, I, J

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	925	0.75	0.78	83	PO4
2	877	0.74	0.78	67	PO4
3	109	0.73	0.94	28	empty
4	189	0.68	0.87	36	empty
5	993	0.67	0.73	94	empty

Interfaces

20 interfaces between chains.

B–A · 2630 Å² buried · 37 hydrogen bonds · protein-protein
I–J · 2621 Å² buried · 43 hydrogen bonds · protein-protein
G–H · 2610 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 2590 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 2076 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

7F2E · SARS-CoV-2 nucleocapsid protein C-terminal domain (dodecamer) · the same entry in another collection · chain E against E, 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 7F2E · PDBe 7F2E · UniProt P0DTC9

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