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Crystal structure of SCTRM10(84)-sah complex

Analyse Crystal structure of SCTRM10(84)-sah complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JWJ
Type: protein
Length: 386 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (GUANINE(9)-N1)-methyltransferase
EC: 2.1.1.221
UniProt: Q12400
Ligands: SAH, SO4
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	TRNA (GUANINE(9)-N1)-methyltransferase (EC 2.1.1.221)	protein	193	41% helix, 18% strand	Q12400

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B

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

Pockets

3 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	196	0.80	0.94	32	SAH
2	202	0.78	0.93	32	SAH
3	52	0.33	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 884 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4JWJ · Crystal structure of scTrm10(84)-SAH complex · the same entry in another collection · chain B against B, TM-score 1.00
Q12400 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(9)-N1)-methyltransferase (Q12400) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 Q12400
Elsewhere: RCSB PDB 4JWJ · PDBe 4JWJ · UniProt Q12400

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