Research workbench

Apra methyltransferase 1 - gnat in complex with MN2+ , SAM, and malonate

Analyse Apra methyltransferase 1 - gnat in complex with MN2+ , SAM, and malonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B3B
Type: protein
Length: 624 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Apra methyltransferase 1
UniProt: A0A1U7N2Z8
Ligands: SAM, MN
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Apra methyltransferase 1	protein	624	50% helix, 15% strand	A0A1U7N2Z8

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · chains A
MN · Manganese (II) ion · metal · chains A
MLI · Malonate ion · additive · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1008	0.78	0.80	83	SAM, MN, MLI, GOL
2	243	0.60	0.80	29	empty
3	251	0.55	0.77	27	empty
4	132	0.46	0.77	20	empty
5	148	0.46	0.76	18	empty

Compared structures

6B3B · AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Malonate · 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 A0A1U7N2Z8
Elsewhere: RCSB PDB 6B3B · PDBe 6B3B · UniProt A0A1U7N2Z8

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