Research workbench
Structure of plasmodium ispc in complex with a beta-thia-isostere derivative of fosmidomycin
Analyse Structure of plasmodium ispc in complex with a beta-thia-isostere derivative of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KP7
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast
- EC
- 1.1.1.267
- UniProt
- O96693
- Ligands
- 1UQ, NAP, MN3
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast (EC 1.1.1.267) | protein | 409 | 51% helix, 15% strand | O96693 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplast (EC 1.1.1.267) | protein | 402 | 52% helix, 16% strand | O96693 |
Ligands and binding sites
- 1UQ · [(S)-({2-[hydroxy(methyl)amino]-2-oxoethyl}sulfanyl)(phenyl)methyl]phosphonic acid · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- MN3 · Manganese (III) ion · metal · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.79 | 0.85 | 68 | MN3, NAP, 1UQ |
| 2 | 90 | 0.76 | 0.97 | 28 | empty |
| 3 | 505 | 0.71 | 0.81 | 63 | 1UQ |
| 4 | 55 | 0.41 | 0.82 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1974 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 4KP7 · Structure of Plasmodium IspC in complex with a beta-thia-isostere derivative of… · the same entry in another collection · chain A against A, TM-score 1.00
- O96693 · AlphaFold monomer V2.0 prediction for 1-deoxy-D-xylulose 5-phosphate reductoisomerase… · a predicted model of the same protein · chain B against A, TM-score 1.00
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 O96693
- Elsewhere: RCSB PDB 4KP7 · PDBe 4KP7 · UniProt O96693
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.