Research workbench

Mouse LIN28A in complex with let-7G microrna pre-element

Analyse Mouse LIN28A in complex with let-7G 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: 3TS2
Type: protein + RNA
Length: 320 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lin-28 homolog a; RNA (5'- R(*GP*GP*GP*GP*UP*CP*UP*AP*UP*GP*AP*UP*AP*CP*CP*AP*CP*C…
UniProt: Q8K3Y3
Ligands: ZN
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein lin-28 homolog a	protein	135	9% helix, 37% strand	Q8K3Y3
B	Protein lin-28 homolog a	protein	137	9% helix, 36% strand	Q8K3Y3
U, V	RNA (5'- R(GPGPGPGPUPCPUPAPUPGPAPUPAPCPCPAPCPCPCPCPGPGP* AP*G)-3')	rna	24	—	—

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

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	405	0.68	0.81	42	empty
2	233	0.67	0.84	34	empty
3	58	0.29	0.75	14	empty
4	53	0.25	0.73	19	empty

Interfaces

4 interfaces between chains.

A–U · 1153 Å² buried · 31 hydrogen bonds · protein-nucleic
B–V · 1133 Å² buried · 27 hydrogen bonds · protein-nucleic
B–U · 781 Å² buried · 18 hydrogen bonds · protein-nucleic
A–V · 708 Å² buried · 18 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

3TS2 · Mouse Lin28A in complex with let-7g microRNA pre-element · the same entry in another collection · chain U against U, 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 B 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 3TS2 · PDBe 3TS2 · UniProt Q8K3Y3

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