MolNFT v1 · #63139 · protein
Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei with hydrolyzed cdp
3F0F · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei…”. X-ray diffraction, 3 ligands (C5P, ZN, MG), 4 pockets (best…
- PDB
- 3F0F
- Type
- protein
- Length
- 474 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
- C5P, ZN, MG
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 159 | 35% helix, 30% strand | Q63T71 |
| C | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 156 | 34% helix, 33% strand | Q63T71 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · chains A, B, C
- GOL · Glycerol · additive · chains A, B
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 | 261 | 0.83 | 0.95 | 50 | MG |
| 2 | 266 | 0.61 | 0.80 | 37 | GOL |
| 3 | 337 | 0.59 | 0.77 | 34 | C5P |
| 4 | 277 | 0.56 | 0.77 | 41 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1154 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1133 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1118 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3F0F · Co-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 3F0F · PDBe 3F0F · UniProt Q63T71
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