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Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthase (ygbp) involved in mevalonate independent isoprenoid biosynthesis

Analyse Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1I52
Type: protein
Length: 225 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-diphosphocytidyl-2-C-methylerythritol synthase
EC: 2.7.7.-
UniProt: Q46893
Ligands: CTP, CA, MG
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-diphosphocytidyl-2-C-methylerythritol synthase (EC 2.7.7.-)	protein	225	34% helix, 25% strand	Q46893

Ligands and binding sites

CTP · Cytidine-5'-triphosphate · ligand · chains A
CA · Calcium ion · metal · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	220	0.53	0.77	28	MG, CTP

Compared structures

1I52 · Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthase (ygbp)… · the same entry in another collection · chain A against A, TM-score 1.00
Q46893 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.97

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q46893
Elsewhere: RCSB PDB 1I52 · PDBe 1I52 · UniProt Q46893

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