MolNFT v1 · #96571 · protein + RNA

Schmallenberg virus nucleoprotein-RNA complex

4JNG · RNA (42-mer): “Schmallenberg virus nucleoprotein-RNA complex”. X-ray diffraction, 10 pockets (best druggability 0.81). MolNFT v1 #96571 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JNG
Type: protein + RNA
Length: 929 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (42-mer); Nucleocapsid protein
UniProt: H2AM13
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 51% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	RNA (42-mer)	rna	42	—	—
A	Nucleocapsid protein	protein	226	53% helix, 8% strand	H2AM13
B	Nucleocapsid protein	protein	214	53% helix, 7% strand	H2AM13
C	Nucleocapsid protein	protein	224	47% helix, 6% strand	H2AM13
D	Nucleocapsid protein	protein	223	50% helix, 5% strand	H2AM13

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	190	0.81	0.96	32	empty
2	171	0.80	0.96	35	empty
3	178	0.79	0.95	36	empty
4	158	0.79	0.96	29	empty
5	980	0.76	0.79	74	empty

Interfaces

8 interfaces between chains.

L–D · 1505 Å² buried · 31 hydrogen bonds · protein-nucleic
L–B · 1505 Å² buried · 33 hydrogen bonds · protein-nucleic
L–A · 1496 Å² buried · 28 hydrogen bonds · protein-nucleic
L–C · 1297 Å² buried · 16 hydrogen bonds · protein-nucleic
A–D · 1185 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4JNG · Schmallenberg virus nucleoprotein-RNA complex · the same entry in another collection · chain L against L, 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 H2AM13
Elsewhere: RCSB PDB 4JNG · PDBe 4JNG · UniProt H2AM13

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