MolNFT v1 · #28820 · protein

Crystal structure of the putative vitamin-B12 independent methionine synthase from listeria monocytogenes, northeast structural genomics target LMR13

1YPX · Putative vitamin-B12 independent methionine synthase family…: “Crystal structure of the putative vitamin-B12 independent methionine synthase from listeria monocytogenes…”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best…

PDB: 1YPX
Type: protein
Length: 318 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative vitamin-B12 independent methionine synthase family protein
UniProt: Q8Y8Q1
Ligands: PO4
Pockets: 4 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative vitamin-B12 independent methionine synthase family protein	protein	318	44% helix, 17% strand	Q8Y8Q1

Ligands and binding sites

PO4 · Phosphate ion · ion · chains A

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.49	0.75	26	empty
2	80	0.38	0.77	15	empty
3	69	0.34	0.76	13	empty
4	83	0.33	0.74	14	empty

Modifications

Observed in the structure: 3 modified (engineered).

Compared structures

1YPX · Crystal Structure of the Putative Vitamin-B12 Independent Methionine Synthase from… · 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 Q8Y8Q1
Elsewhere: RCSB PDB 1YPX · PDBe 1YPX · UniProt Q8Y8Q1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.