MolNFT v1 · #25457 · protein
Crystal structure of 3-deoxy-D-arabino-heptulosonate-7- phosphate synthase (dahp synthase) from aeropyrum pernix in complex with MN2+ and pep
1VS1 · 3-deoxy-7-phosphoheptulonate synthase: “Crystal structure of 3-deoxy-D-arabino-heptulosonate-7- phosphate synthase (dahp synthase) from aeropyrum…”. X-ray diffraction, 2 ligands (PEP, MN), 12 pockets (best druggability 0.74). MolNFT…
- PDB
- 1VS1
- Type
- protein
- Length
- 1,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-7-phosphoheptulonate synthase
- EC
- 2.5.1.54
- UniProt
- Q9YEJ7
- Ligands
- PEP, MN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) | protein | 270 | 41% helix, 19% strand | Q9YEJ7 |
| B | 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) | protein | 267 | 41% helix, 19% strand | Q9YEJ7 |
| C | 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) | protein | 268 | 40% helix, 19% strand | Q9YEJ7 |
| D | 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) | protein | 271 | 39% helix, 18% strand | Q9YEJ7 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.74 | 0.99 | 18 | empty |
| 2 | 59 | 0.72 | 0.98 | 18 | empty |
| 3 | 718 | 0.71 | 0.78 | 92 | PEP |
| 4 | 682 | 0.70 | 0.78 | 84 | PEP |
| 5 | 225 | 0.47 | 0.74 | 34 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1536 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1504 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1440 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1416 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 155 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1VS1 · Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase)… · 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 Q9YEJ7
- Elsewhere: RCSB PDB 1VS1 · PDBe 1VS1 · UniProt Q9YEJ7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.