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Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase dsrbd in complex with a 22 nucleotide dsrna

Analyse Crystal structure of human tRNA-DIHYDROURIDINE(20) synthase dsrbd in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OC6
Type: protein + RNA
Length: 112 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like; RNA
EC: 1.3.1.-
UniProt: Q9NX74
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like (EC 1.3.1.-)	protein	90	32% helix, 26% strand	Q9NX74
B, C	RNA	rna	11	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.53	0.75	17	empty

Interfaces

3 interfaces between chains.

B–C · 439 Å² buried · 47 hydrogen bonds · nucleic-nucleic
A–C · 368 Å² buried · 8 hydrogen bonds · protein-nucleic
A–B · 308 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

5OC6 · Crystal structure of human tRNA-dihydrouridine(20) synthase dsRBD in complex with a 22… · the same entry in another collection · chain A against A, TM-score 1.00
Q9NX74 · AlphaFold monomer V2.0 prediction for tRNA-DIHYDROURIDINE(20) synthase [NAD(P)+]-like… · a predicted model of the same protein · chain A against A, TM-score 0.98

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Every structure of UniProt Q9NX74
Elsewhere: RCSB PDB 5OC6 · PDBe 5OC6 · UniProt Q9NX74

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