MolNFT v1 · #171666 · protein

Coxsackievirus B4 in complex with capsid binder compound 48

6ZCK · Genome polyprotein: “Coxsackievirus B4 in complex with capsid binder compound 48”. Electron microscopy, 2 ligands (QFW, MYR), 9 pockets (best druggability 0.75). MolNFT v1 #171666 on GenesisL1: 3D structure, binding sites and…

PDB: 6ZCK
Type: protein
Length: 819 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
EC: 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
UniProt: Q8V639
Ligands: QFW, MYR
Pockets: 9 · best druggability 0.75

Structure

electron microscopy · 4 distinct chains · 9% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48)	protein	271	9% helix, 31% strand	Q8V639
B	Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48)	protein	252	9% helix, 36% strand	Q8V639
C	Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48)	protein	238	9% helix, 30% strand	Q8V639
D	Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48)	protein	58	7% helix, 16% strand	Q8V639

Ligands and binding sites

QFW · 2-oxidanyl-4-[(6-propoxynaphthalen-2-yl) sulfonylamino]benzoic acid · ligand · chains A, C
MYR · Myristic acid · ligand · chains D

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

Pockets

9 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	415	0.75	0.85	66	empty
2	220	0.47	0.74	34	empty
3	118	0.46	0.78	19	empty
4	70	0.43	0.81	23	empty
5	88	0.41	0.78	22	empty

Interfaces

6 interfaces between chains.

A–C · 4431 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 2130 Å² buried · 36 hydrogen bonds · protein-protein
B–C · 1666 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1295 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 946 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 lipid (myristoylation).

Compared structures

6ZCK · Coxsackievirus B4 in complex with capsid binder compound 48 · 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 Q8V639
Elsewhere: RCSB PDB 6ZCK · PDBe 6ZCK · UniProt Q8V639

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