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Poliovirus (type 1 mahoney), receptor-catalysed 135S particle incubated with anti-VP1 mab at rt for 1 hr

Analyse Poliovirus (type 1 mahoney), receptor-catalysed 135S particle incubated with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q0B
Type: protein
Length: 1,160 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; Anti-VP1…
UniProt: P03300
Ligands: MYR
Pockets: 17 · best druggability 0.79

Structure

electron microscopy · 5 distinct chains · 8% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Capsid protein VP1	protein	191	10% helix, 40% strand	P03300
2	Capsid protein VP2	protein	234	12% helix, 35% strand	P03300
3	Capsid protein VP3	protein	228	11% helix, 23% strand	P03300
4	Capsid protein VP4	protein	68	10% helix, 12% strand	P03300
7	Anti-VP1 mab	protein	439	3% helix, 21% strand	—

Ligands and binding sites

MYR · Myristic acid · ligand · chains 4

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	780	0.79	0.83	73	empty
2	290	0.66	0.82	51	empty
3	343	0.61	0.78	65	empty
4	191	0.61	0.82	41	empty
5	190	0.60	0.82	50	empty

Interfaces

4 interfaces between chains.

1–3 · 2203 Å² buried · 33 hydrogen bonds · protein-protein
2–3 · 1633 Å² buried · 16 hydrogen bonds · protein-protein
1–2 · 961 Å² buried · 13 hydrogen bonds · protein-protein
3–7 · 38 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 lipid (myristoylation).

Compared structures

6Q0B · Poliovirus (Type 1 Mahoney), receptor-catalysed 135S particle incubated with anti-VP1 mAb… · 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 P03300
Elsewhere: RCSB PDB 6Q0B · PDBe 6Q0B · UniProt P03300

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