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Structure of mycobacterium tuberculosis dxr in complex with a fosmidomycin analogue
Analyse Structure of mycobacterium tuberculosis dxr in complex with a fosmidomycin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZHX
- Type
- protein
- Length
- 751 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
- FM6, MN
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 372 | 49% helix, 16% strand | P64012 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 379 | 46% helix, 16% strand | P64012 |
Ligands and binding sites
- FM6 · [(1S)-1-(3,4-dichlorophenyl)-3-[oxidanyl(phenylcarbonyl)amino]propyl]phosphonic acid · ligand · chains A
- 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
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 | 523 | 0.68 | 0.79 | 88 | MN, FM6 |
| 2 | 492 | 0.67 | 0.78 | 55 | MN |
| 3 | 97 | 0.40 | 0.77 | 21 | empty |
| 4 | 51 | 0.39 | 0.81 | 14 | empty |
| 5 | 110 | 0.39 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1799 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3ZHX · Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue · the same entry in another collection · chain B against B, 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 3ZHX · PDBe 3ZHX · UniProt P64012
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