MolNFT v1 · #117254 · protein
3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis in complex with D-phenylalanine
5E2L · 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase: “3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis in complex with…”. X-ray diffraction, 4 ligands (DPN, MN, SO4), 14 pockets (best druggability…
- PDB
- 5E2L
- Type
- protein
- Length
- 920 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
- DPN, MN, SO4, CL
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% 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 | 42% helix, 14% strand | A0A0E8NFD1 |
| B | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (EC 2.5.1.54) | protein | 458 | 44% helix, 15% strand | A0A0E8NFD1 |
Ligands and binding sites
- DPN · D-phenylalanine · 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
- CL · Chloride ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.77 | 0.79 | 88 | GOL |
| 2 | 209 | 0.70 | 0.87 | 39 | DPN |
| 3 | 127 | 0.69 | 0.91 | 26 | DPN |
| 4 | 403 | 0.65 | 0.79 | 51 | CL |
| 5 | 457 | 0.63 | 0.76 | 45 | SO4, CL |
Interfaces
1 interface between chains.
- A–B · 1880 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5E2L · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in… · 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 A0A0E8NFD1
- Elsewhere: RCSB PDB 5E2L · PDBe 5E2L · UniProt A0A0E8NFD1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.