MolNFT v1 · #115091 · protein

Crystal structure of empty coxsackievirus A16 particle

5C9A · VP1: “Crystal structure of empty coxsackievirus A16 particle”. X-ray diffraction, 3 ligands (SPH, K, CL), 14 pockets (best druggability 0.84). MolNFT v1 #115091 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5C9A
Type: protein
Length: 819 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP0; VP3
UniProt: I3W9E1
Ligands: SPH, K, CL
Pockets: 14 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	282	12% helix, 29% strand	I3W9E1
B	VP0	protein	295	13% helix, 32% strand	I3W9E1
C	VP3	protein	242	12% helix, 31% strand	I3W9E1

Ligands and binding sites

SPH · Sphingosine · ligand · chains A, C
K · Potassium ion · metal · chains A, C
CL · Chloride ion · ion · 7 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	398	0.84	0.92	55	SPH
2	70	0.49	0.84	14	empty
3	167	0.47	0.76	26	CL
4	157	0.44	0.76	32	empty
5	65	0.44	0.82	15	empty

Interfaces

3 interfaces between chains.

A–C · 4054 Å² buried · 67 hydrogen bonds · protein-protein
A–B · 3501 Å² buried · 60 hydrogen bonds · protein-protein
B–C · 2570 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

5C9A · Crystal structure of empty coxsackievirus A16 particle · 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 I3W9E1
Elsewhere: RCSB PDB 5C9A · PDBe 5C9A · UniProt I3W9E1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.