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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
- 3ZI0
- Type
- protein
- Length
- 730 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
- FM8, MN
- Pockets
- 7 · best druggability 0.67
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 | 357 | 47% helix, 16% strand | P64012 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 373 | 48% helix, 17% strand | P64012 |
Ligands and binding sites
- FM8 · [(1S)-1-(3,4-dichlorophenyl)-3-{hydroxy[2-(1H-1,2,4-triazol-1-ylmethyl)benzoyl]amino}propyl]phosphonic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains B
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 | 525 | 0.67 | 0.78 | 56 | MN |
| 2 | 411 | 0.64 | 0.78 | 53 | FM8 |
| 3 | 93 | 0.41 | 0.77 | 21 | empty |
| 4 | 113 | 0.39 | 0.75 | 22 | empty |
| 5 | 78 | 0.38 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1734 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3ZI0 · Structure of Mycobacterium tuberculosis DXR in complex with a fosmidomycin analogue · 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 3ZI0 · PDBe 3ZI0 · UniProt P64012
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