MolNFT v1 · #73209 · protein
The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free)
3NV8 · Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate…: “The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate…”. X-ray diffraction, 5 ligands (PEP, MN, SO4), 10 pockets (best…
- PDB
- 3NV8
- Type
- protein
- Length
- 926 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
- PEP, MN, SO4, CL, PO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% 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 | 462 | 43% helix, 15% strand | O53512 |
| B | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase arog (EC 2.5.1.54) | protein | 464 | 43% helix, 15% strand | O53512 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · chains B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.82 | 0.89 | 71 | GOL |
| 2 | 1083 | 0.76 | 0.78 | 84 | GOL |
| 3 | 541 | 0.69 | 0.79 | 68 | SO4 |
| 4 | 388 | 0.64 | 0.78 | 55 | empty |
| 5 | 305 | 0.62 | 0.80 | 42 | SO4, PO4 |
Interfaces
1 interface between chains.
- A–B · 1919 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 3NV8 · The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with… · 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 3NV8 · PDBe 3NV8 · UniProt O53512
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.