MolNFT v1 · #57934 · protein
Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) complexed with 5-phenylpyridin-2-ylmethylphosphonic acid
3ANM: “Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) complexed with…”. X-ray diffraction, 2 ligands (SYD, NDP), 6 pockets (best druggability 0.74). MolNFT v1 #57934 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3ANM
- Type
- protein
- Length
- 798 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- EC
- 1.1.1.267
- UniProt
- P45568
- Ligands
- SYD, NDP
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 400 | 51% helix, 15% strand | P45568 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 398 | 52% helix, 15% strand | P45568 |
Ligands and binding sites
- SYD · [(5-phenylpyridin-2-yl)methyl]phosphonic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.74 | 0.90 | 35 | empty |
| 2 | 676 | 0.74 | 0.80 | 76 | SYD, NDP |
| 3 | 641 | 0.73 | 0.80 | 63 | SYD, NDP |
| 4 | 79 | 0.35 | 0.76 | 20 | empty |
| 5 | 60 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1633 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3ANM · Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P45568 · 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 0.96
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 P45568
- Elsewhere: RCSB PDB 3ANM · PDBe 3ANM · UniProt P45568
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