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PP7 coat protein dimer in complex with RNA hairpin

Analyse PP7 coat protein dimer in complex with RNA hairpin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2QUX
Type: protein + RNA
Length: 1,602 residues
Chains: 18
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (25-mer); Coat protein
UniProt: Q38062
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 8 distinct chains · 21% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, F, I, L, O, R	RNA (25-mer)	rna	25	—	—
A, G, J	Coat protein	protein	123	20% helix, 47% strand	Q38062
B	Coat protein	protein	121	21% helix, 50% strand	Q38062
D, E, P	Coat protein	protein	122	20% helix, 45% strand	Q38062
H, N	Coat protein	protein	119	21% helix, 48% strand	Q38062
K	Coat protein	protein	122	20% helix, 46% strand	Q38062
M	Coat protein	protein	119	21% helix, 50% strand	Q38062
Q	Coat protein	protein	117	21% helix, 43% strand	Q38062

Ligands and binding sites

GOL · Glycerol · additive · 15 copies · chains I, G, L, J, R, P, A, B, D, H, E, K

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	818	0.77	0.81	47	empty
2	944	0.76	0.80	65	GOL
3	949	0.76	0.79	61	empty
4	1103	0.75	0.78	62	empty
5	971	0.75	0.79	51	empty

Interfaces

31 interfaces between chains.

J–K · 3209 Å² buried · 50 hydrogen bonds · protein-protein
P–Q · 3207 Å² buried · 55 hydrogen bonds · protein-protein
D–E · 3196 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3188 Å² buried · 50 hydrogen bonds · protein-protein
G–H · 3171 Å² buried · 48 hydrogen bonds · protein-protein

Compared structures

2QUX · PP7 coat protein dimer in complex with RNA hairpin · the same entry in another collection · chain C against C, 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 Q38062
Elsewhere: RCSB PDB 2QUX · PDBe 2QUX · UniProt Q38062

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