Research workbench
Arabidopsis thaliana ispd in complex with tribromodichloro-pseudilin
Analyse Arabidopsis thaliana ispd in complex with tribromodichloro-pseudilin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NAL
- Type
- protein
- Length
- 213 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
- EC
- 2.7.7.60
- UniProt
- P69834
- Ligands
- H70, K, CD
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 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 | 213 | 34% helix, 23% strand | P69834 |
Ligands and binding sites
- H70 · 2,4-dichloro-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol · ligand · chains A
- K · Potassium ion · metal · 7 copies · chains A
- CD · Cadmium ion · metal · 5 copies · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · 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 | 292 | 0.68 | 0.83 | 30 | H70, CD |
| 2 | 54 | 0.29 | 0.75 | 17 | empty |
Compared structures
- 4NAL · Arabidopsis thaliana IspD in complex with tribromodichloro-pseudilin · 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 0.96
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 4NAL · PDBe 4NAL · UniProt P69834
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