MolNFT v1 · #19884 · protein
Crystal structure of chorismate synthase complexed with oxidized FMN and epsp
1QXO: “Crystal structure of chorismate synthase complexed with oxidized FMN and epsp”. X-ray diffraction, 3 ligands (NCO, FMN, EPS), 20 pockets (best druggability 0.85). MolNFT v1 #19884 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1QXO
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chorismate synthase
- EC
- 4.2.3.5
- UniProt
- P0A2Y6
- Ligands
- NCO, FMN, EPS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chorismate synthase (EC 4.2.3.5) | protein | 388 | 38% helix, 21% strand | P0A2Y6 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 9 copies · chains A, C, B, D
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D
- EPS · 5-[(1-carboxyvinyl)oxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.85 | 0.94 | 56 | FMN, EPS |
| 2 | 388 | 0.84 | 0.93 | 57 | FMN, EPS |
| 3 | 394 | 0.84 | 0.92 | 48 | FMN, EPS |
| 4 | 1017 | 0.81 | 0.82 | 116 | EDO |
| 5 | 705 | 0.78 | 0.83 | 73 | FMN, EPS |
Interfaces
6 interfaces between chains.
- C–D · 4676 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4634 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 2067 Ų buried · 39 hydrogen bonds · protein-protein
- B–D · 2064 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 864 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 1QXO · Crystal structure of Chorismate synthase complexed with oxidized FMN and EPSP · the same entry in another collection · chain D against D, TM-score 1.00
- P0A2Y6 · AlphaFold monomer V2.0 prediction for chorismate synthase (P0A2Y6) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P0A2Y6
- Elsewhere: RCSB PDB 1QXO · PDBe 1QXO · UniProt P0A2Y6
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