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Trmb complex with sah

Analyse Trmb complex with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NZI
Type: protein
Length: 413 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: SAH
Pockets: 4 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	207	40% helix, 20% strand	O34522
B	TRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33)	protein	206	39% helix, 19% strand	O34522

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 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	228	0.59	0.80	27	SAH
2	220	0.58	0.80	37	SAH
3	65	0.36	0.78	20	GOL
4	51	0.34	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 838 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7NZI · TrmB complex with SAH · 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 7NZI · PDBe 7NZI · UniProt O34522

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