MolNFT v1 · #58139 · protein
Crystal structure of the quaternary complex-1 of an isomerase
3AU9 · 1-deoxy-D-xylulose 5-phosphate reductoisomerase: “Crystal structure of the quaternary complex-1 of an isomerase”. X-ray diffraction, 4 ligands (NDP, FOM, MG), 3 pockets (best druggability 0.76). MolNFT v1 #58139 on GenesisL1: 3D…
- PDB
- 3AU9
- Type
- protein
- Length
- 820 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- UniProt
- O96693
- Ligands
- NDP, FOM, MG, CA
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | protein | 410 | 50% helix, 15% strand | O96693 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FOM · 3-[formyl(hydroxy)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.76 | 0.86 | 64 | NDP, FOM |
| 2 | 372 | 0.74 | 0.85 | 60 | NDP, FOM |
| 3 | 88 | 0.48 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1986 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 3AU9 · Crystal structure of the quaternary complex-1 of an isomerase · 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 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 O96693
- Elsewhere: RCSB PDB 3AU9 · PDBe 3AU9 · UniProt O96693
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