Research workbench
X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, dxr, RV2870C, from mycobacterium tuberculosis, in complex with a 3,4- dichlorophenyl-substituted fosmidomycin analogue, manganese and NADPH.
Analyse X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, dxr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y1F
- Type
- protein
- Length
- 752 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
- A2VLK3
- Ligands
- NDP, 34F, MN, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 373 | 48% helix, 16% strand | A2VLK3 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 379 | 47% helix, 16% strand | A2VLK3 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 34F · (1S)-1-(3,4-dichlorophenyl)-3-[formyl(hydroxy)amino]propyl}phosphonic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.73 | 0.78 | 88 | SO4, NDP |
| 2 | 537 | 0.71 | 0.80 | 80 | 34F, NDP, MN |
| 3 | 130 | 0.41 | 0.75 | 25 | empty |
| 4 | 96 | 0.41 | 0.77 | 19 | empty |
| 5 | 82 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1731 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2Y1F · X-ray structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from… · the same entry in another collection · chain A 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 A2VLK3
- Elsewhere: RCSB PDB 2Y1F · PDBe 2Y1F · UniProt A2VLK3
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