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Crystal structure of authentic providence virus

Analyse Crystal structure of authentic providence virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QQP
Type: protein + RNA
Length: 2,191 residues
Chains: 9
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Large capsid protein; Small capsid protein; RNA (5'-R(*UP*UP*UP*U)-3')
UniProt: Q80IX5
Ligands: CA
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 8 distinct chains · 17% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Large capsid protein	protein	484	14% helix, 40% strand	Q80IX5
B	Small capsid protein	protein	39	62% helix, 0% strand	Q80IX5
D	Small capsid protein	protein	40	58% helix, 3% strand	Q80IX5
E	Large capsid protein	protein	517	10% helix, 36% strand	Q80IX5
F	Small capsid protein	protein	67	57% helix, 0% strand	Q80IX5
G	Large capsid protein	protein	518	12% helix, 37% strand	Q80IX5
H	Small capsid protein	protein	38	66% helix, 0% strand	Q80IX5
R	RNA (5'-R(UPUPUPU)-3')	rna	4	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, C, E, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.88	0.93	70	empty
2	1110	0.87	0.88	122	empty
3	992	0.86	0.86	130	empty
4	715	0.85	0.89	64	empty
5	234	0.85	0.98	31	CA

Interfaces

19 interfaces between chains.

C–E · 2551 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 2059 Å² buried · 45 hydrogen bonds · protein-protein
E–G · 2041 Å² buried · 36 hydrogen bonds · protein-protein
A–E · 1979 Å² buried · 33 hydrogen bonds · protein-protein
C–G · 1626 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

2QQP · Crystal Structure of Authentic Providence Virus · 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 Q80IX5
Elsewhere: RCSB PDB 2QQP · PDBe 2QQP · UniProt Q80IX5

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