MolNFT v1 · #31831 · protein
The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis
2B7O · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog: “The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis”. X-ray diffraction, 4 ligands (PEP, CE1, MN), 16 pockets (best…
- PDB
- 2B7O
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog
- EC
- 2.5.1.54
- UniProt
- O53512
- Ligands
- PEP, CE1, MN, SO4
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 451 | 43% helix, 14% strand | O53512 |
| B | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 451 | 44% helix, 13% strand | O53512 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- CE1 · O-dodecanyl octaethylene glycol · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.81 | 0.87 | 64 | CE1 |
| 2 | 793 | 0.75 | 0.80 | 67 | empty |
| 3 | 569 | 0.69 | 0.78 | 69 | empty |
| 4 | 159 | 0.63 | 0.85 | 25 | SO4, PEP |
| 5 | 304 | 0.61 | 0.79 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1954 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 modified (engineered).
Compared structures
- 2B7O · The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- O53512 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase arog… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O53512
- Elsewhere: RCSB PDB 2B7O · PDBe 2B7O · UniProt O53512
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