Research workbench
Crystal structure of 2-amino-2-desoxyisochorismate synthase (adic) synthase phze from burkholderia lata 383 in complex with benzoate, pyruvate, glutamine and contaminating ZN2+
Analyse Crystal structure of 2-amino-2-desoxyisochorismate synthase (adic) synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R75
- Type
- protein
- Length
- 1,238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ANTHRANILATE/PARA-aminobenzoate synthases component I
- EC
- 4.1.3.27
- UniProt
- Q396C7
- Ligands
- BEZ, PYR, MG, ZN, PO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ANTHRANILATE/PARA-aminobenzoate synthases component I (EC 4.1.3.27) | protein | 616 | 31% helix, 32% strand | Q396C7 |
| B | ANTHRANILATE/PARA-aminobenzoate synthases component I (EC 4.1.3.27) | protein | 622 | 31% helix, 31% strand | Q396C7 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.73 | 0.99 | 21 | BEZ, PYR |
| 2 | 57 | 0.73 | 0.99 | 21 | BEZ, PYR |
| 3 | 70 | 0.58 | 0.89 | 22 | empty |
| 4 | 365 | 0.56 | 0.75 | 68 | empty |
| 5 | 79 | 0.34 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 4076 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3R75 · Crystal structure of 2-amino-2-desoxyisochorismate synthase (ADIC) synthase PhzE from… · 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 Q396C7
- Elsewhere: RCSB PDB 3R75 · PDBe 3R75 · UniProt Q396C7
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