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Crystal structure of human NSUN6/TRNA

Analyse Crystal structure of human NSUN6/TRNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WWT
Type: protein + RNA
Length: 1,062 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative methyltransferase NSUN6; TRNA
EC: 2.1.1.-
UniProt: Q8TEA1
Pockets: 19 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	461	32% helix, 23% strand	Q8TEA1
C	TRNA	rna	72	—	—
D	TRNA	rna	71	—	—
B	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	458	32% helix, 23% strand	Q8TEA1

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	573	0.82	0.88	58	empty
2	994	0.81	0.83	77	empty
3	498	0.78	0.86	52	empty
4	90	0.74	0.97	19	empty
5	82	0.71	0.95	14	empty

Interfaces

3 interfaces between chains.

A–C · 2211 Å² buried · 46 hydrogen bonds · protein-nucleic
D–B · 2198 Å² buried · 47 hydrogen bonds · protein-nucleic
A–B · 1022 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

5WWT · Crystal structure of human NSun6/tRNA · the same entry in another collection · chain A against A, TM-score 1.00
Q8TEA1 · AlphaFold monomer V2.0 prediction for tRNA (CYTOSINE(72)-C(5))-methyltransferase NSUN6… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8TEA1
Elsewhere: RCSB PDB 5WWT · PDBe 5WWT · UniProt Q8TEA1

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