MolNFT v1 · #10314 · protein
Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthetase (ygbp) involved in mevalonate independent isoprenoid biosynthesis, complexed with cdp-me and MG2+
1INI · 4-diphosphocytidyl-2-C-methylerythritol synthetase: “Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthetase (ygbp) involved in…”. X-ray diffraction, 2 ligands (CDM, MG), 1 pocket (best druggability 0.53).…
- PDB
- 1INI
- 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 synthetase
- EC
- 2.7.7.-
- UniProt
- Q46893
- Ligands
- CDM, MG
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-diphosphocytidyl-2-C-methylerythritol synthetase (EC 2.7.7.-) | protein | 225 | 32% helix, 25% strand | Q46893 |
Ligands and binding sites
- CDM · 4-diphosphocytidyl-2-C-methyl-D-erythritol · ligand · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.53 | 0.78 | 28 | MG, CDM |
Compared structures
- 1INI · Crystal structure of 4-diphosphocytidyl-2-C-methylerythritol (cdp-me) synthetase (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
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 Q46893
- Elsewhere: RCSB PDB 1INI · PDBe 1INI · UniProt Q46893
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