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Crystal structure of pyrococcus abyssi TRM5A complexed with adenosine

Analyse Crystal structure of pyrococcus abyssi TRM5A complexed with adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HJI
Type: protein
Length: 349 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (GUANINE(37)-N1)-methyltransferase TRM5A
EC: 2.1.1.228
UniProt: Q9V2G1
Ligands: ADN
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (GUANINE(37)-N1)-methyltransferase TRM5A (EC 2.1.1.228)	protein	349	33% helix, 33% strand	Q9V2G1

Ligands and binding sites

ADN · Adenosine · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.77	0.86	54	ADN
2	165	0.39	0.72	26	empty
3	74	0.35	0.76	17	empty

Compared structures

5HJI · Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine · the same entry in another collection · chain A against A, TM-score 1.00
Q9V2G1 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(37)-N1)/4-DEMETHYLWYOSINE(37)-methyltr… · a predicted model of the same protein · chain A against A, TM-score 0.77

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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 Q9V2G1
Elsewhere: RCSB PDB 5HJI · PDBe 5HJI · UniProt Q9V2G1

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