Research workbench
Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)
Analyse Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MRO
- Type
- protein
- Length
- 215 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Arabidopsis thaliana
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
- EC
- 2.7.7.60
- UniProt
- P69834
- Ligands
- Q9P, CD, K
- Pockets
- 2 · best druggability 0.74
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic (EC 2.7.7.60) | protein | 215 | 34% helix, 23% strand | P69834 |
Ligands and binding sites
- Q9P · Azolopyrimidine · ligand · chains A
- CD · Cadmium ion · metal · 3 copies · chains A
- K · Potassium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.74 | 0.95 | 22 | Q9P |
| 2 | 93 | 0.36 | 0.75 | 15 | empty |
Compared structures
- 5MRO · Arabidopsis thaliana ispd GLU258ALA mutant in complex with azolopyrimidine (1) · the same entry in another collection · chain A against A, TM-score 1.00
- P69834 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 4-phosphate… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P69834
- Elsewhere: RCSB PDB 5MRO · PDBe 5MRO · UniProt P69834
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