Research workbench

P domain of GII.3-TV24

Analyse P domain of GII.3-TV24 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IR5
Type: protein
Length: 1,209 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1 capsid protein
UniProt: Q66296
Pockets: 15 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1 capsid protein	protein	301	6% helix, 36% strand	Q66296
B	VP1 capsid protein	protein	302	6% helix, 36% strand	Q66296
C	VP1 capsid protein	protein	304	6% helix, 36% strand	Q66296
D	VP1 capsid protein	protein	302	7% helix, 36% strand	Q66296

Pockets

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	127	0.79	0.97	41	empty
2	129	0.78	0.96	45	empty
3	970	0.73	0.77	110	empty
4	185	0.68	0.87	28	empty
5	200	0.65	0.84	28	empty

Interfaces

3 interfaces between chains.

A–C · 1845 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1806 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 782 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6IR5 · P domain of GII.3-TV24 · the same entry in another collection · chain A against A, 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 Q66296
Elsewhere: RCSB PDB 6IR5 · PDBe 6IR5 · UniProt Q66296

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