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The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan
Analyse The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NUE
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog
- EC
- 2.5.1.54
- UniProt
- O53512
- Ligands
- TRP, CE1, MN, SO4, PO4, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 453 | 44% helix, 13% strand | O53512 |
| B | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 443 | 45% helix, 12% strand | O53512 |
Ligands and binding sites
- TRP · Tryptophan · 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 · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.80 | 0.87 | 71 | SO4, CE1 |
| 2 | 950 | 0.77 | 0.79 | 86 | TRP, GOL |
| 3 | 496 | 0.67 | 0.79 | 68 | PO4, MN |
| 4 | 341 | 0.62 | 0.79 | 45 | empty |
| 5 | 366 | 0.62 | 0.78 | 45 | SO4, GOL |
Interfaces
1 interface between chains.
- A–B · 2164 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NUE · The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium… · the same entry in another collection · chain B against B, 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 3NUE · PDBe 3NUE · UniProt O53512
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