MolNFT v1 · #114711 · protein

Crystal structure of magnesium-bound DUF89 protein saccharomyces cerevisiae

5BY0 · Protein-glutamate O-methyltransferase: “Crystal structure of magnesium-bound DUF89 protein saccharomyces cerevisiae”. X-ray diffraction, 1 ligand (MG), 2 pockets (best druggability 0.66). MolNFT v1 #114711 on GenesisL1: 3D…

PDB: 5BY0
Type: protein
Length: 465 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein-glutamate O-methyltransferase
EC: 2.1.1.-
UniProt: Q04371
Ligands: MG
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein-glutamate O-methyltransferase (EC 2.1.1.-)	protein	465	57% helix, 10% strand	Q04371

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

2 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	348	0.66	0.80	43	empty
2	151	0.43	0.75	20	empty

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

5BY0 · Crystal structure of magnesium-bound Duf89 protein Saccharomyces cerevisiae · the same entry in another collection · chain A against A, TM-score 1.00
Q04371 · AlphaFold monomer V2.0 prediction for damage-control phosphatase YMR027W (Q04371) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q04371
Elsewhere: RCSB PDB 5BY0 · PDBe 5BY0 · UniProt Q04371

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