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Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of arabidopsis thaliana
Analyse Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PMP
- Type
- protein
- Length
- 160 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q9CAK8
- Ligands
- C5P, ZN, PO4, CL
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 160 | 34% helix, 31% strand | Q9CAK8 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.39 | 0.75 | 18 | ZN |
Compared structures
- 2PMP · Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9CAK8 · 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 0.98
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 Q9CAK8
- Elsewhere: RCSB PDB 2PMP · PDBe 2PMP · UniProt Q9CAK8
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