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Crystal structure of ybxf bound to the SAM-I riboswitch aptamer

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

PDB: 3V7E
Type: protein + RNA
Length: 410 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome-associated protein L7AE-like; SAM-I riboswitch aptamer with an engineered helix…
UniProt: P46350
Ligands: NCO, SAM, MG
Pockets: 12 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosome-associated protein L7AE-like	protein	81	44% helix, 25% strand	P46350
B	Ribosome-associated protein L7AE-like	protein	77	25% helix, 8% strand	P46350
C, D	SAM-I riboswitch aptamer with an engineered helix P3	rna	126	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 18 copies · chains C, D
SAM · S-adenosylmethionine · ligand · 2 copies · chains C, D
MG · Magnesium ion · metal · 22 copies · chains C, D

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

Pockets

12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.79	0.82	55	NCO, SAM, MG
2	901	0.78	0.82	56	NCO, SAM, MG
3	746	0.68	0.77	49	NCO
4	742	0.63	0.74	33	NCO
5	304	0.59	0.79	36	NCO

Interfaces

5 interfaces between chains.

A–C · 437 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 384 Å² buried · 7 hydrogen bonds · protein-nucleic
C–D · 167 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 77 Å² buried · 0 hydrogen bonds · protein-nucleic
A–D · 72 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

3V7E · Crystal structure of YbxF bound to the SAM-I riboswitch aptamer · the same entry in another collection · chain A against A, TM-score 1.00
P46350 · AlphaFold monomer V2.0 prediction for ribosome-associated protein L7AE-like (P46350) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P46350
Elsewhere: RCSB PDB 3V7E · PDBe 3V7E · UniProt P46350

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