MolNFT v1 · #85041 · protein
Crystal structure of mycobacterium tuberculosis dxr in complex with the antibiotic FR900098 and cofactor NADPH
4A03 · 1-deoxy-D-xylulose 5-phosphate reductoisomerase: “Crystal structure of mycobacterium tuberculosis dxr in complex with the antibiotic FR900098 and cofactor NADPH”. X-ray diffraction, 3 ligands (F98, NDP, MN), 7 pockets (best…
- PDB
- 4A03
- Type
- protein
- Length
- 756 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
- P64012
- Ligands
- F98, NDP, MN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 378 | 48% helix, 16% strand | P64012 |
Ligands and binding sites
- F98 · 3-[ethanoyl(hydroxy)amino]propylphosphonic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.73 | 0.83 | 76 | MN, F98, NDP |
| 2 | 426 | 0.73 | 0.83 | 76 | MN, F98, NDP |
| 3 | 110 | 0.40 | 0.75 | 23 | empty |
| 4 | 105 | 0.36 | 0.74 | 16 | empty |
| 5 | 82 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4A03 · Crystal Structure of Mycobacterium tuberculosis DXR in complex with the antibiotic… · 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 P64012
- Elsewhere: RCSB PDB 4A03 · PDBe 4A03 · UniProt P64012
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