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the wildtype SAM-VI riboswitch bound to SAM

Analyse the wildtype SAM-VI riboswitch bound to SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LAS
Type: protein + RNA
Length: 381 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.708
Source: Homo sapiens; SYNTHETIC CONSTRUCT
Molecule: RNA (55-mer); U1 small nuclear ribonucleoprotein A
UniProt: P09012
Ligands: SAM
Pockets: 9 · best druggability 0.69

Structure

x-ray diffraction · resolution 2.708 · 4 distinct chains · 33% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (55-mer)	rna	55	—	—
C	U1 small nuclear ribonucleoprotein A	protein	91	29% helix, 26% strand	P09012
E	U1 small nuclear ribonucleoprotein A	protein	93	34% helix, 25% strand	P09012
D	U1 small nuclear ribonucleoprotein A	protein	87	36% helix, 26% strand	P09012

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

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

Pockets

9 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	535	0.69	0.79	58	empty
2	634	0.68	0.78	38	empty
3	503	0.67	0.79	28	empty
4	113	0.49	0.81	16	empty
5	218	0.45	0.74	18	SAM

Interfaces

6 interfaces between chains.

A–E · 1202 Å² buried · 42 hydrogen bonds · protein-nucleic
B–C · 1156 Å² buried · 40 hydrogen bonds · protein-nucleic
A–D · 672 Å² buried · 16 hydrogen bonds · protein-nucleic
C–D · 450 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 98 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 11 modified (engineered).

Compared structures

6LAS · The wildtype SAM-VI riboswitch bound to SAM · the same entry in another collection · chain E against E, TM-score 1.00
P09012 · AlphaFold monomer V2.0 prediction for U1 small nuclear ribonucleoprotein a (P09012) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P09012
Elsewhere: RCSB PDB 6LAS · PDBe 6LAS · UniProt P09012

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