MolNFT v1 · #135940 · protein + RNA

Human LIN28A in complex with let-7F-1 microrna pre-element

5UDZ · Protein lin-28 homolog a: “Human LIN28A in complex with let-7F-1 microrna pre-element”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.58). MolNFT v1 #135940 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5UDZ
Type: protein + RNA
Length: 325 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein lin-28 homolog a; Let-7F-1 pre-element
UniProt: Q9H9Z2
Ligands: ZN
Pockets: 7 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein lin-28 homolog a	protein	139	12% helix, 36% strand	Q9H9Z2
V	Let-7F-1 pre-element	rna	24	—	—
W	Let-7F-1 pre-element	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	477	0.58	0.74	53	empty
2	79	0.49	0.84	18	empty
3	52	0.42	0.83	14	empty
4	54	0.42	0.83	13	empty
5	54	0.40	0.81	15	empty

Interfaces

4 interfaces between chains.

A–V · 1307 Å² buried · 32 hydrogen bonds · protein-nucleic
B–W · 1220 Å² buried · 19 hydrogen bonds · protein-nucleic
B–V · 828 Å² buried · 25 hydrogen bonds · protein-nucleic
A–W · 815 Å² buried · 23 hydrogen bonds · protein-nucleic

Compared structures

5UDZ · Human LIN28A in complex with let-7f-1 microRNA pre-element · the same entry in another collection · chain A against A, TM-score 1.00
Q9H9Z2 · AlphaFold monomer V2.0 prediction for protein lin-28 homolog a (Q9H9Z2) · 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 Q9H9Z2
Elsewhere: RCSB PDB 5UDZ · PDBe 5UDZ · UniProt Q9H9Z2

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