MolNFT v1 · #118276 · protein
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites
5EX4 · 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase: “3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with…”. X-ray diffraction, 5 ligands (TRP, MN, SO4), 13 pockets (best druggability…
- PDB
- 5EX4
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
- EC
- 2.5.1.54
- UniProt
- A0A0E8NFD1
- Ligands
- TRP, MN, SO4, PO4, CL
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 462 | 44% helix, 15% strand | A0A0E8NFD1 |
| B | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 462 | 45% helix, 15% strand | A0A0E8NFD1 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 5 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.82 | 0.90 | 51 | TRP, GOL |
| 2 | 953 | 0.77 | 0.80 | 84 | TRP, GOL |
| 3 | 393 | 0.64 | 0.78 | 41 | empty |
| 4 | 433 | 0.63 | 0.77 | 44 | TRP, CL |
| 5 | 298 | 0.61 | 0.79 | 38 | PO4 |
Interfaces
1 interface between chains.
- A–B · 2074 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5EX4 · 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis… · 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 A0A0E8NFD1
- Elsewhere: RCSB PDB 5EX4 · PDBe 5EX4 · UniProt A0A0E8NFD1
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