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The structure of xanthosine methyltransferase

Analyse The structure of xanthosine methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EG5
Type: protein
Length: 1,377 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xanthosine methyltransferase
EC: 2.1.1.-
UniProt: A4GE69
Ligands: SAH, XTS
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Xanthosine methyltransferase (EC 2.1.1.-)	protein	344	44% helix, 19% strand	A4GE69
E	Xanthosine methyltransferase (EC 2.1.1.-)	protein	346	43% helix, 18% strand	A4GE69
G	Xanthosine methyltransferase (EC 2.1.1.-)	protein	343	44% helix, 19% strand	A4GE69

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, C, E, G
XTS · 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-purine-2,6-dione · ligand · 4 copies · chains A, C, E, G

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

Pockets

18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	521	0.75	0.83	56	SAH, XTS
2	502	0.75	0.83	49	SAH, XTS
3	484	0.74	0.83	48	SAH, XTS
4	532	0.74	0.82	63	SAH, XTS
5	435	0.68	0.80	35	empty

Interfaces

3 interfaces between chains.

E–G · 1101 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1089 Å² buried · 11 hydrogen bonds · protein-protein
C–G · 232 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

2EG5 · The structure of xanthosine methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
A4GE69 · AlphaFold monomer V2.0 prediction for 7-methylxanthosine synthase 1 (A4GE69) · a predicted model of the same protein · chain G 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 A4GE69
Elsewhere: RCSB PDB 2EG5 · PDBe 2EG5 · UniProt A4GE69

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