Research workbench
Crystal structure of 2C-methyl-D-erythritol 2,4- clycodiphosphate synthase complexed with ligand
Analyse Crystal structure of 2C-methyl-D-erythritol 2,4- clycodiphosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EOR
- Type
- protein
- Length
- 157 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
- P62617
- Ligands
- CFV, GPP, NA, ZN
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 29% 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 | 157 | 33% helix, 29% strand | P62617 |
Ligands and binding sites
- CFV · [(2R)-1-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-propan-2-yl]oxymethylphosphonic acid · ligand · chains A
- GPP · Geranyl diphosphate · ligand · chains A
- NA · Sodium ion · metal · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.45 | 0.78 | 22 | ZN, NA |
Compared structures
- 3EOR · Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with… · 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 0.97
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 P62617
- Elsewhere: RCSB PDB 3EOR · PDBe 3EOR · UniProt P62617
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