Research workbench
M. tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase bound to 1-deoxy-L-erythrulose
Analyse M. tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RCV
- Type
- protein
- Length
- 747 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
- I6YAH0
- Ligands
- NDP, DE2, MN, PO3
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 47% 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 | 370 | 48% helix, 16% strand | I6YAH0 |
| B | 1-deoxy-D-xylulose 5-phosphate reductoisomerase (EC 1.1.1.267) | protein | 377 | 46% helix, 16% strand | I6YAH0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- DE2 · 1-deoxy-L-erythrulose · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- PO3 · Phosphite ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.71 | 0.78 | 82 | NDP, PO3 |
| 2 | 480 | 0.66 | 0.78 | 68 | MN, NDP, DE2, PO3 |
| 3 | 50 | 0.49 | 0.86 | 15 | empty |
| 4 | 129 | 0.42 | 0.75 | 23 | empty |
| 5 | 94 | 0.38 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1708 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4RCV · M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase bound to… · 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 I6YAH0
- Elsewhere: RCSB PDB 4RCV · PDBe 4RCV · UniProt I6YAH0
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