MolNFT v1 · #183652 · protein

Trmb complex with SAM

7NYB · TRNA (guanine-N(7)-)-methyltransferase: “Trmb complex with SAM”. X-ray diffraction, 1 ligand (SAM), 5 pockets (best druggability 0.59). MolNFT v1 #183652 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7NYB
Type: protein
Length: 410 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (guanine-N(7)-)-methyltransferase
EC: 2.1.1.33
UniProt: O34522
Ligands: SAM
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	206	42% helix, 19% strand	O34522
B	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	204	42% helix, 19% strand	O34522

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

5 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	223	0.59	0.80	29	SAM
2	228	0.59	0.80	30	SAM
3	90	0.42	0.79	23	empty
4	77	0.39	0.78	22	empty
5	64	0.30	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 832 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7NYB · TrmB complex with SAM · the same entry in another collection · chain A against A, TM-score 1.00
O34522 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(7)-)-methyltransferase (O34522) · a predicted model of the same protein · chain A 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 O34522
Elsewhere: RCSB PDB 7NYB · PDBe 7NYB · UniProt O34522

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