MolNFT v1 · #122997 · protein
Crystal structure of DAH7PS-cm complex from geobacillus sp. with prephenate
5J6F · 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase…: “Crystal structure of DAH7PS-cm complex from geobacillus sp. with prephenate”. X-ray diffraction, 3 ligands (PRE, MN, SO4), 5 pockets (best druggability 0.65). MolNFT v1 #122997…
- PDB
- 5J6F
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
- EC
- 2.5.1.54, 5.4.99.5
- UniProt
- L8A208
- Ligands
- PRE, MN, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3 (EC 2.5.1.54, 5.4.99.5) | protein | 352 | 50% helix, 14% strand | L8A208 |
| B | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3 (EC 2.5.1.54, 5.4.99.5) | protein | 340 | 49% helix, 14% strand | L8A208 |
Ligands and binding sites
- PRE · Prephenic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.65 | 0.84 | 31 | SO4 |
| 2 | 227 | 0.64 | 0.83 | 31 | SO4 |
| 3 | 505 | 0.62 | 0.75 | 56 | empty |
| 4 | 107 | 0.54 | 0.83 | 15 | PRE |
| 5 | 109 | 0.52 | 0.82 | 15 | PRE |
Interfaces
1 interface between chains.
- A–B · 1406 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5J6F · Crystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate · 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 L8A208
- Elsewhere: RCSB PDB 5J6F · PDBe 5J6F · UniProt L8A208
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