Research workbench
Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase
Analyse Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GX1
- Type
- protein
- Length
- 471 residues
- Chains
- 3
- 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
- P36663
- Ligands
- CDP, ZN, MN, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 157 | 35% helix, 31% strand | P36663 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, C, B
- SO4 · Sulfate ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.85 | 0.97 | 33 | SO4 |
| 2 | 455 | 0.68 | 0.80 | 45 | CDP, MN |
| 3 | 337 | 0.67 | 0.81 | 36 | ZN, CDP, MN |
| 4 | 349 | 0.64 | 0.80 | 33 | CDP, MN |
Interfaces
3 interfaces between chains.
- A–B · 1071 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1070 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1058 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1GX1 · Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase · the same entry in another collection · chain A against A, TM-score 1.00
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 P36663
- Elsewhere: RCSB PDB 1GX1 · PDBe 1GX1 · UniProt P36663
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