Research workbench
M. tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase W203Y mutant bound to fosmidomycin and NADPH
Analyse M. tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase W203Y mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OOE
- Type
- protein
- Length
- 1,509 residues
- Chains
- 4
- 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
- I6YAH0
- Ligands
- FOM, NDP, MN
- Pockets
- 17 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% 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 | 376 | 49% helix, 16% strand | I6YAH0 |
| B, D | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 378 | 48% helix, 16% strand | I6YAH0 |
| C | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 377 | 49% helix, 16% strand | I6YAH0 |
Ligands and binding sites
- FOM · 3-[formyl(hydroxy)amino]propylphosphonic acid · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.74 | 0.84 | 71 | FOM, MN, NDP |
| 2 | 383 | 0.74 | 0.85 | 72 | FOM, NDP |
| 3 | 423 | 0.73 | 0.83 | 71 | FOM, NDP |
| 4 | 389 | 0.73 | 0.84 | 71 | FOM, NDP |
| 5 | 201 | 0.47 | 0.75 | 26 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1767 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1701 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 216 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 136 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4OOE · M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W203Y mutant bound to… · 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 I6YAH0
- Elsewhere: RCSB PDB 4OOE · PDBe 4OOE · UniProt I6YAH0
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