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Structure of METTL6 bound with SAM

Analyse Structure of METTL6 bound with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F1E
Type: protein
Length: 474 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA N(3)-methylcytidine methyltransferase METTL6
EC: 2.1.1.-
UniProt: Q8TCB7
Ligands: SAM
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA N(3)-methylcytidine methyltransferase METTL6 (EC 2.1.1.-)	protein	244	36% helix, 30% strand	Q8TCB7
B	TRNA N(3)-methylcytidine methyltransferase METTL6 (EC 2.1.1.-)	protein	230	33% helix, 31% strand	Q8TCB7

Ligands and binding sites

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

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	330	0.67	0.81	42	SAM
2	263	0.64	0.81	43	SAM
3	267	0.49	0.74	31	empty
4	79	0.32	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 486 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

7F1E · Structure of METTL6 bound with SAM · the same entry in another collection · chain B against B, TM-score 1.00
Q8TCB7 · AlphaFold monomer V2.0 prediction for tRNA N(3)-methylcytidine methyltransferase METTL6… · a predicted model of the same protein · chain B against A, TM-score 0.98

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q8TCB7
Elsewhere: RCSB PDB 7F1E · PDBe 7F1E · UniProt Q8TCB7

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