Research workbench

Mouse Lin28A in complex with let-7f-1 microRNA pre-element

Analyse Mouse Lin28A in complex with let-7f-1 microRNA pre-element in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TS0
Type: protein + RNA
Length: 318 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.763
Source: Mus musculus; SYNTHETIC CONSTRUCT
Molecule: Protein lin-28 homolog A; RNA (5'-R(*GP*GP*GP*GP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*AP*CP*CP*CP…
UniProt: Q8K3Y3
Ligands: ZN
Pockets: 7 · best druggability 0.52

Structure

x-ray diffraction · resolution 2.763 · 2 distinct chains · 7% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein lin-28 homolog A	protein	136	7% helix, 37% strand	Q8K3Y3
U, V	RNA (5'-R(GPGPGPGPUPAPGPUPGPAPUPUPUPUPAPCPCPCPUPGPGPAP*G)-3')	rna	23	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.52	0.86	20	empty
2	245	0.48	0.74	33	empty
3	99	0.42	0.78	16	empty
4	85	0.41	0.78	16	empty
5	139	0.38	0.74	18	empty

Interfaces

4 interfaces between chains.

B–V · 1285 Å² buried · 29 hydrogen bonds · protein-nucleic
A–U · 1250 Å² buried · 24 hydrogen bonds · protein-nucleic
B–U · 829 Å² buried · 21 hydrogen bonds · protein-nucleic
A–V · 822 Å² buried · 23 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

3TS0 · Mouse LIN28A in complex with let-7F-1 microrna pre-element · the same entry in another collection · chain A against A, TM-score 1.00
Q8K3Y3 · AlphaFold monomer V2.0 prediction for protein lin-28 homolog a (Q8K3Y3) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q8K3Y3
Elsewhere: RCSB PDB 3TS0 · PDBe 3TS0 · UniProt Q8K3Y3

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