MolNFT v1 · #138858 · protein + RNA

Crystal structure of human NSUN6/TRNA/SAM

5WWS: “Crystal structure of human NSUN6/TRNA/SAM”. X-ray diffraction, 1 ligand (SAM), 17 pockets (best druggability 0.82). MolNFT v1 #138858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5WWS
Type: protein + RNA
Length: 1,060 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA; Putative methyltransferase NSUN6
EC: 2.1.1.-
UniProt: Q8TEA1
Ligands: SAM
Pockets: 17 · best druggability 0.82

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	TRNA	rna	72	—	—
D	TRNA	rna	71	—	—
A	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	460	32% helix, 23% strand	Q8TEA1
B	Putative methyltransferase NSUN6 (EC 2.1.1.-)	protein	457	32% helix, 23% strand	Q8TEA1

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains C, A, D, B

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

Pockets

17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	520	0.82	0.89	52	empty
2	808	0.76	0.81	63	SAM
3	787	0.75	0.80	60	SAM
4	464	0.71	0.81	41	empty
5	806	0.71	0.77	63	empty

Interfaces

3 interfaces between chains.

D–B · 2236 Å² buried · 45 hydrogen bonds · protein-nucleic
C–A · 2214 Å² buried · 45 hydrogen bonds · protein-nucleic
A–B · 1026 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

5WWS · Crystal structure of human NSun6/tRNA/SAM · the same entry in another collection · chain C against C, 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 5WWS · PDBe 5WWS · UniProt Q8TEA1

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