MolNFT v1 · #104254 · protein

High-resolution crystal structure of coxsackievirus A24V

4Q4W · Coxsackievirus capsid protein VP1: “High-resolution crystal structure of coxsackievirus A24V”. X-ray diffraction, 2 ligands (CA, CL), 15 pockets (best druggability 0.74). MolNFT v1 #104254 on GenesisL1: 3D structure, binding sites…

PDB: 4Q4W
Type: protein
Length: 836 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coxsackievirus capsid protein VP1; Coxsackievirus capsid protein VP2; Coxsackievirus…
UniProt: V9VEF3
Ligands: CA, CL
Pockets: 15 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Coxsackievirus capsid protein VP1	protein	281	12% helix, 31% strand	V9VEF3
2	Coxsackievirus capsid protein VP2	protein	264	15% helix, 36% strand	V9VEF3
3	Coxsackievirus capsid protein VP3	protein	234	8% helix, 30% strand	V9VEF3
4	Coxsackievirus capsid protein VP4	protein	57	12% helix, 16% strand	V9VEF3

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains 1, 4, 2
CL · Chloride ion · ion · 4 copies · chains 1, 2
HEZ · Hexane-1,6-diol · additive · 3 copies · chains 1, 3, 2

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

Pockets

15 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	391	0.74	0.84	58	empty
2	135	0.59	0.84	26	empty
3	77	0.54	0.86	19	empty
4	64	0.50	0.85	16	empty
5	201	0.47	0.75	33	empty

Interfaces

6 interfaces between chains.

1–3 · 3945 Å² buried · 73 hydrogen bonds · protein-protein
1–2 · 2441 Å² buried · 43 hydrogen bonds · protein-protein
2–3 · 1729 Å² buried · 20 hydrogen bonds · protein-protein
1–4 · 1025 Å² buried · 12 hydrogen bonds · protein-protein
3–4 · 901 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4Q4W · High-resolution crystal structure of Coxsackievirus A24v · the same entry in another collection · chain 1 against 1, 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 V9VEF3
Elsewhere: RCSB PDB 4Q4W · PDBe 4Q4W · UniProt V9VEF3

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