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Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to sah and M7G-capped RNA

Analyse Crystal structure of the zebrafish cap-specific adenosine methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IRZ
Type: protein
Length: 467 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PDX1 C-terminal-inhibiting factor 1
UniProt: A0A0R4IKJ1
Ligands: SAH, M7G
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PDX1 C-terminal-inhibiting factor 1	protein	467	49% helix, 13% strand	A0A0R4IKJ1

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A
EDO · 1,2-ethanediol · additive · 3 copies · 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	887	0.78	0.81	113	SAH, EDO, M7G
2	51	0.30	0.76	12	empty
3	59	0.27	0.73	11	empty

Compared structures

6IRZ · Crystal structure of the zebrafish cap-specific adenosine methyltransferase bound to SAH… · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A0R4IKJ1
Elsewhere: RCSB PDB 6IRZ · PDBe 6IRZ · UniProt A0A0R4IKJ1

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