MolNFT v1 · #117301 · protein
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site
5E40 · 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase: “3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis with D-tyrosine bound in…”. X-ray diffraction, 3 ligands (DTY, MN, SO4), 11 pockets (best…
- PDB
- 5E40
- Type
- protein
- Length
- 918 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
- DTY, MN, SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 462 | 43% helix, 14% strand | A0A0E8NFD1 |
| B | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 456 | 43% helix, 15% strand | A0A0E8NFD1 |
Ligands and binding sites
- DTY · D-tyrosine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.77 | 0.79 | 81 | GOL |
| 2 | 210 | 0.72 | 0.88 | 35 | DTY |
| 3 | 263 | 0.66 | 0.83 | 43 | DTY |
| 4 | 358 | 0.65 | 0.80 | 42 | SO4 |
| 5 | 444 | 0.64 | 0.77 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 1825 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5E40 · 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with… · 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 5E40 · PDBe 5E40 · UniProt A0A0E8NFD1
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