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Structure of seneca valley virus-001

Analyse Structure of seneca valley virus-001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CJI
Type: protein
Length: 799 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyprotein
UniProt: Q155Z9
Ligands: CA
Pockets: 10 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyprotein	protein	258	9% helix, 32% strand	Q155Z9
B	Polyprotein	protein	238	8% helix, 33% strand	Q155Z9
C	Polyprotein	protein	268	13% helix, 37% strand	Q155Z9
D	Polyprotein	protein	35	11% helix, 14% strand	Q155Z9

Ligands and binding sites

CA · Calcium ion · metal · chains B

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	210	0.69	0.86	29	empty
2	374	0.64	0.79	43	empty
3	334	0.61	0.78	53	empty
4	199	0.49	0.76	33	empty
5	163	0.48	0.77	26	empty

Interfaces

6 interfaces between chains.

A–B · 3400 Å² buried · 51 hydrogen bonds · protein-protein
A–C · 2807 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 1736 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 924 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 560 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3CJI · Structure of Seneca Valley Virus-001 · 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 Q155Z9
Elsewhere: RCSB PDB 3CJI · PDBe 3CJI · UniProt Q155Z9

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