Research workbench
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028
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
- 3Q8H
- Type
- protein
- Length
- 464 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
- AO9, ZN, K
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 32% 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 | 151 | 35% helix, 34% strand | Q63T71 |
| B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 155 | 34% helix, 33% strand | Q63T71 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 34% helix, 30% strand | Q63T71 |
Ligands and binding sites
- AO9 · 5'-deoxy-5'-[(imidazo[2,1-b][1,3]thiazol-5-ylcarbonyl)amino]cytidine · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- K · Potassium ion · metal · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.82 | 0.94 | 49 | K |
| 2 | 184 | 0.54 | 0.79 | 30 | AO9 |
| 3 | 192 | 0.53 | 0.78 | 30 | AO9 |
| 4 | 190 | 0.51 | 0.77 | 36 | AO9 |
Interfaces
3 interfaces between chains.
- A–C · 1205 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1160 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1144 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3Q8H · 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 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 Q63T71
- Elsewhere: RCSB PDB 3Q8H · PDBe 3Q8H · UniProt Q63T71
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