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Hexameric crystal structure of schmallenberg virus nucleoprotein

Analyse Hexameric crystal structure of schmallenberg virus nucleoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4IDX
Type: protein
Length: 640 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nucleocapsid protein
UniProt: H2AM13
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Nucleocapsid protein	protein	209	47% helix, 4% strand	H2AM13
A	Nucleocapsid protein	protein	218	43% helix, 5% strand	H2AM13
C	Nucleocapsid protein	protein	213	45% helix, 3% strand	H2AM13

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	787	0.73	0.78	50	empty
2	507	0.66	0.78	53	empty
3	429	0.61	0.76	47	empty
4	402	0.60	0.76	39	empty
5	216	0.59	0.80	40	empty

Interfaces

3 interfaces between chains.

B–C · 568 Å² buried · 0 hydrogen bonds · protein-protein
B–A · 399 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 129 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4IDX · hexameric crystal structure of Schmallenberg virus nucleoprotein · the same entry in another collection · chain C against C, 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 4IDX · PDBe 4IDX · UniProt H2AM13

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