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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with 5'-iodo- 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
- 3K2X
- Type
- protein
- Length
- 454 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
- Q3JRA0
- Ligands
- I5A, ZN, K, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 33% 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 | 154 | 34% helix, 31% strand | Q3JRA0 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 153 | 35% helix, 32% strand | Q3JRA0 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 147 | 36% helix, 35% strand | Q3JRA0 |
Ligands and binding sites
- I5A · 5'-deoxy-5'-iodocytidine · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- K · Potassium 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 | 243 | 0.81 | 0.94 | 48 | K |
| 2 | 248 | 0.57 | 0.78 | 36 | I5A |
| 3 | 207 | 0.48 | 0.75 | 31 | I5A |
| 4 | 84 | 0.34 | 0.75 | 25 | I5A |
Interfaces
3 interfaces between chains.
- B–C · 1151 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1129 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1099 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3K2X · 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
- Q3JRA0 · 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 0.99
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 Q3JRA0
- Elsewhere: RCSB PDB 3K2X · PDBe 3K2X · UniProt Q3JRA0
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