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RNA stemloop from bacteriophage qbeta complexed with an N87S mutant MS2 capsid

Analyse RNA stemloop from bacteriophage qbeta complexed with an N87S mutant MS2 capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZSE
Type: protein + RNA
Length: 399 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA hairpin; Coat protein
UniProt: P03612
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	RNA hairpin	rna	12	—	—
A, B, C	Coat protein	protein	129	19% helix, 47% strand	P03612

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	417	0.63	0.78	39	empty
2	485	0.62	0.75	53	empty
3	212	0.57	0.80	26	empty
4	90	0.35	0.75	23	empty
5	58	0.29	0.74	14	empty

Interfaces

4 interfaces between chains.

A–B · 3281 Å² buried · 48 hydrogen bonds · protein-protein
A–C · 516 Å² buried · 8 hydrogen bonds · protein-protein
R–A · 374 Å² buried · 8 hydrogen bonds · protein-nucleic
R–B · 279 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

1ZSE · RNA stemloop from bacteriophage Qbeta complexed with an N87S mutant MS2 Capsid · the same entry in another collection · chain R against R, 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 P03612
Elsewhere: RCSB PDB 1ZSE · PDBe 1ZSE · UniProt P03612

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