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Crystal structure of mycobacterium tuberculosis dxr in complex with the antibiotic FR900098 and cofactor NADPH
Analyse Crystal structure of mycobacterium tuberculosis dxr in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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