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Crystal structure of 4-amino-4-deoxychorismate lyase from pseudomonas aeruginosa
Analyse Crystal structure of 4-amino-4-deoxychorismate lyase from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y4R
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-amino-4-deoxychorismate lyase
- EC
- 4.1.3.38
- UniProt
- Q9HZN6
- Ligands
- PLP, CL, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-amino-4-deoxychorismate lyase (EC 4.1.3.38) | protein | 270 | 29% helix, 32% strand | Q9HZN6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.81 | 0.97 | 33 | empty |
| 2 | 480 | 0.78 | 0.86 | 57 | PLP, GOL |
| 3 | 547 | 0.76 | 0.84 | 61 | GOL, PLP |
| 4 | 72 | 0.41 | 0.80 | 18 | empty |
| 5 | 70 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2172 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2Y4R · Crystal structure of 4-amino-4-deoxychorismate lyase from pseudomonas aeruginosa · 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 Q9HZN6
- Elsewhere: RCSB PDB 2Y4R · PDBe 2Y4R · UniProt Q9HZN6
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