MolNFT v1 · #11829 · protein

2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf)

1JY8: “2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (ispf)”. X-ray diffraction, 3 ligands (C5P, CDI, ZN), 1 pocket (best druggability 0.37). MolNFT v1 #11829 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JY8
Type: protein
Length: 155 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
UniProt: P62617
Ligands: C5P, CDI, ZN
Pockets: 1 · best druggability 0.37

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase	protein	155	36% helix, 31% strand	P62617

Ligands and binding sites

C5P · Cytidine-5'-monophosphate · ligand · chains A
CDI · 2C-methyl-D-erythritol 2,4-cyclodiphosphate · ligand · chains A
ZN · Zinc 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	61	0.37	0.79	17	CDI

Compared structures

1JY8 · 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) · the same entry in another collection · chain A against A, TM-score 1.00
P62617 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P62617
Elsewhere: RCSB PDB 1JY8 · PDBe 1JY8 · UniProt P62617

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