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X-ray structure of the HRV2 empty capsid (B-particle)

Analyse X-ray structure of the HRV2 empty capsid (B-particle) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TN9
Type: protein
Length: 707 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein VP1; Protein VP2; Protein VP3
UniProt: P04936
Pockets: 9 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Protein VP1	protein	222	10% helix, 32% strand	P04936
2	Protein VP2	protein	248	11% helix, 37% strand	P04936
3	Protein VP3	protein	237	10% helix, 30% strand	P04936

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	166	0.67	0.87	32	empty
2	220	0.50	0.75	40	empty
3	121	0.49	0.80	19	empty
4	79	0.45	0.81	26	empty
5	199	0.45	0.74	33	empty

Interfaces

3 interfaces between chains.

1–3 · 3087 Å² buried · 45 hydrogen bonds · protein-protein
1–2 · 1758 Å² buried · 35 hydrogen bonds · protein-protein
2–3 · 1705 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

3TN9 · X-ray structure of the HRV2 empty capsid (B-particle) · 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 P04936
Elsewhere: RCSB PDB 3TN9 · PDBe 3TN9 · UniProt P04936

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