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SARS-cov-2 programmed -1 frameshifting element three stem H-type pseudoknot

Analyse SARS-cov-2 programmed -1 frameshifting element three stem H-type pseudoknot in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MLX
Type: protein + RNA
Length: 494 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BL3-6 Fab heavy chain; BL3-6 Fab light chain; RNA (65-mer)
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	BL3-6 Fab heavy chain	protein	216	10% helix, 51% strand	—
L	BL3-6 Fab light chain	protein	213	6% helix, 51% strand	—
R	RNA (65-mer)	rna	65	—	—

Pockets

6 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	616	0.62	0.75	35	empty
2	430	0.59	0.75	57	empty
3	360	0.56	0.75	39	empty
4	95	0.37	0.75	24	empty
5	77	0.32	0.74	20	empty

Interfaces

3 interfaces between chains.

H–L · 1825 Å² buried · 16 hydrogen bonds · protein-protein
H–R · 654 Å² buried · 15 hydrogen bonds · protein-nucleic
L–R · 119 Å² buried · 2 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7MLX · SARS-CoV-2 programmed -1 frameshifting element three stem H-type pseudoknot · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 7MLX · PDBe 7MLX

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