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Bovine enterovirus F3 in complex with a cysteinylglycine dipeptide

Analyse Bovine enterovirus F3 in complex with a cysteinylglycine dipeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T40
Type: protein
Length: 806 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3; VP4
UniProt: Q2LKZ0
Ligands: GLY, STE, CYS, K, SO4, CL
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	271	12% helix, 33% strand	Q2LKZ0
B	VP2	protein	244	14% helix, 38% strand	Q2LKZ0
C	VP3	protein	243	9% helix, 30% strand	Q2LKZ0
D	VP4	protein	48	15% helix, 8% strand	Q2LKZ0

Ligands and binding sites

GLY · Glycine · ligand · chains A
STE · Stearic acid · ligand · chains A, C
CYS · Cysteine · ligand · chains A, C
K · Potassium ion · metal · 4 copies · chains A, D, B, C
SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
CL · Chloride ion · ion · 2 copies · chains C
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	335	0.84	0.94	46	STE
2	285	0.59	0.78	42	K
3	133	0.46	0.78	24	empty
4	136	0.44	0.76	30	empty
5	87	0.44	0.80	16	empty

Interfaces

6 interfaces between chains.

A–C · 4003 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 2159 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 1673 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1330 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 964 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6T40 · Bovine enterovirus F3 in complex with a Cysteinylglycine dipeptide · the same entry in another collection · chain B against B, 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 Q2LKZ0
Elsewhere: RCSB PDB 6T40 · PDBe 6T40 · UniProt Q2LKZ0

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