MolNFT v1 · #101929 · protein

2.8A crystal structure of lymphocytic choriomeningitis virus nucleoprotein C-terminal domain

4O6H: “2.8A crystal structure of lymphocytic choriomeningitis virus nucleoprotein C-terminal domain”. X-ray diffraction, 3 ligands (ZN, MG, K), 17 pockets (best druggability 0.80). MolNFT v1 #101929 on GenesisL1: 3D structure, binding…

PDB: 4O6H
Type: protein
Length: 1,611 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleoprotein
UniProt: P09992
Ligands: ZN, MG, K
Pockets: 17 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, G, H	Nucleoprotein	protein	203	42% helix, 19% strand	P09992
B, D	Nucleoprotein	protein	204	39% helix, 18% strand	P09992
E	Nucleoprotein	protein	196	41% helix, 16% strand	P09992
F	Nucleoprotein	protein	195	40% helix, 17% strand	P09992

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 4 copies · chains C, D, G, H
K · Potassium ion · metal · 4 copies · chains C, D, G, H
IMD · Imidazole · additive · 4 copies · chains A, B, E, F

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.80	0.85	58	empty
2	718	0.80	0.84	71	empty
3	505	0.72	0.81	63	empty
4	476	0.70	0.81	60	empty
5	437	0.70	0.81	50	empty

Interfaces

8 interfaces between chains.

A–D · 991 Å² buried · 15 hydrogen bonds · protein-protein
F–H · 958 Å² buried · 13 hydrogen bonds · protein-protein
B–F · 545 Å² buried · 1 hydrogen bond · protein-protein
A–E · 507 Å² buried · 4 hydrogen bonds · protein-protein
C–H · 372 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4O6H · 2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal… · 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 P09992
Elsewhere: RCSB PDB 4O6H · PDBe 4O6H · UniProt P09992

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