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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with cytosine
Analyse Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKE
- Type
- protein
- Length
- 459 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
- Q63T71
- Ligands
- CYT, ZN, MG, CL
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 35% 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 | 158 | 35% helix, 30% strand | Q63T71 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 153 | 35% helix, 30% strand | Q63T71 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 148 | 35% helix, 33% strand | Q63T71 |
Ligands and binding sites
- CYT · 6-aminopyrimidin-2(1H)-one · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A, B, C
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.82 | 0.93 | 49 | MG |
| 2 | 263 | 0.64 | 0.81 | 38 | ZN, CYT |
| 3 | 207 | 0.47 | 0.75 | 36 | CYT |
| 4 | 202 | 0.46 | 0.74 | 29 | CYT |
Interfaces
3 interfaces between chains.
- A–B · 1145 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1140 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1099 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3IKE · Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q63T71 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain C 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 Q63T71
- Elsewhere: RCSB PDB 3IKE · PDBe 3IKE · UniProt Q63T71
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