MolNFT v1 · #58138 · protein
Crystal structure of the ternary complex of an isomerase
3AU8 · 1-deoxy-D-xylulose 5-phosphate reductoisomerase: “Crystal structure of the ternary complex of an isomerase”. X-ray diffraction, 2 ligands (NDP, MN), 5 pockets (best druggability 0.73). MolNFT v1 #58138 on GenesisL1: 3D structure…
- PDB
- 3AU8
- Type
- protein
- Length
- 804 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, MN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | protein | 399 | 51% helix, 16% strand | O96693 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | protein | 405 | 52% helix, 16% strand | O96693 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.73 | 0.97 | 28 | empty |
| 2 | 492 | 0.65 | 0.77 | 48 | NDP, MN |
| 3 | 495 | 0.64 | 0.77 | 48 | NDP, MN |
| 4 | 79 | 0.33 | 0.74 | 16 | NDP |
| 5 | 53 | 0.28 | 0.75 | 14 | NDP |
Interfaces
1 interface between chains.
- A–B · 1956 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3AU8 · Crystal structure of the ternary complex 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 A against A, TM-score 0.97
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 3AU8 · PDBe 3AU8 · UniProt O96693
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