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Crystal structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from shewanella oneidensis
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
- 1T0A
- Type
- protein
- Length
- 474 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q8EBR3
- Ligands
- FPP, ZN, CO
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 158 | 35% helix, 32% strand | Q8EBR3 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- CO · Cobalt (II) ion · metal · 3 copies · chains A, B, C
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 | 227 | 0.85 | 0.97 | 32 | FPP |
| 2 | 270 | 0.64 | 0.81 | 34 | CO |
| 3 | 294 | 0.62 | 0.80 | 44 | CO |
| 4 | 281 | 0.62 | 0.80 | 42 | CO |
Interfaces
3 interfaces between chains.
- B–C · 1045 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1012 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1008 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1T0A · Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8EBR3 · 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 Q8EBR3
- Elsewhere: RCSB PDB 1T0A · PDBe 1T0A · UniProt Q8EBR3
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