MolNFT v1 · #67244 · protein
Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with cytidine
3IEQ · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with…”. X-ray diffraction, 4 ligands (C, ZN, MG), 4 pockets (best…
- PDB
- 3IEQ
- 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
- C, 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, 32% strand | Q63T71 |
Ligands and binding sites
- C · Cytidine-5'-monophosphate · ligand · 3 copies · chains A, C, B
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.82 | 0.94 | 51 | MG |
| 2 | 297 | 0.66 | 0.82 | 40 | C |
| 3 | 259 | 0.51 | 0.75 | 30 | C |
| 4 | 199 | 0.45 | 0.74 | 34 | C, ZN |
Interfaces
3 interfaces between chains.
- B–C · 1159 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1131 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3IEQ · 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 3IEQ · PDBe 3IEQ · UniProt Q63T71
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