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Crystal structure of human NSUN6/TRNA/SFG

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

PDB: 5WWR
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
Ligands: SFG
Pockets: 16 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	461	31% helix, 23% strand	Q8TEA1
B	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	457	33% helix, 23% strand	Q8TEA1
C, D	TRNA	rna	72	—	—

Ligands and binding sites

SFG · Sinefungin · ligand · 2 copies · chains A, C, B, D

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

Pockets

16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.82	0.87	61	empty
2	809	0.76	0.81	61	SFG
3	945	0.76	0.80	74	empty
4	781	0.75	0.81	62	SFG
5	1193	0.74	0.78	90	empty

Interfaces

3 interfaces between chains.

B–D · 2203 Å² buried · 42 hydrogen bonds · protein-nucleic
A–C · 2202 Å² buried · 43 hydrogen bonds · protein-nucleic
A–B · 1026 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5WWR · Crystal structure of human NSun6/tRNA/SFG · 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 5WWR · PDBe 5WWR · UniProt Q8TEA1

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