MolNFT v1 · #129718 · protein

Crystal structure of bovine enterovirus 2 determined with serial femtosecond X-ray crystallography

5OSN · Capsid protein: “Crystal structure of bovine enterovirus 2 determined with serial femtosecond X-ray crystallography”. X-ray diffraction, 5 ligands (SPH, GLU, OSF), 13 pockets (best druggability 0.86). MolNFT v1 #129718 on GenesisL1…

PDB: 5OSN
Type: protein
Length: 793 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: Q65480
Ligands: SPH, GLU, OSF, K, SO4
Pockets: 13 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	270	12% helix, 32% strand	Q65480
B	Capsid protein	protein	237	13% helix, 38% strand	Q65480
C	Capsid protein	protein	243	8% helix, 30% strand	Q65480
D	Capsid protein	protein	43	16% helix, 7% strand	Q65480

Ligands and binding sites

SPH · Sphingosine · ligand · chains A, C
GLU · Glutamic acid · ligand · chains A, C
OSF · octyl sulfate · ligand · chains C
K · Potassium ion · metal · 3 copies · chains A, D, C
SO4 · Sulfate ion · ion · chains C

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

Pockets

13 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	420	0.86	0.93	55	SPH
2	254	0.61	0.80	41	K
3	172	0.51	0.78	40	empty
4	92	0.45	0.80	18	empty
5	54	0.44	0.83	13	empty

Interfaces

6 interfaces between chains.

A–C · 4005 Å² buried · 72 hydrogen bonds · protein-protein
A–B · 2155 Å² buried · 30 hydrogen bonds · protein-protein
B–C · 1699 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1337 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1011 Å² buried · 16 hydrogen bonds · protein-protein

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 Q65480
Elsewhere: RCSB PDB 5OSN · PDBe 5OSN · UniProt Q65480

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