Research workbench
Anthranilate phosphoribosyltransferase in complex with prpp, anthranilate and magnesium
Analyse Anthranilate phosphoribosyltransferase in complex with prpp, anthranilate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZYK
- Type
- protein
- Length
- 1,375 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P50384
- Ligands
- BE2, PRP, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 344 | 53% helix, 13% strand | P50384 |
| C | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 343 | 53% helix, 13% strand | P50384 |
Ligands and binding sites
- BE2 · 2-aminobenzoic acid · ligand · 8 copies · chains A, B, C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.79 | 0.84 | 62 | MG, PRP, BE2 |
| 2 | 613 | 0.77 | 0.83 | 55 | MG, PRP, BE2 |
| 3 | 614 | 0.76 | 0.83 | 49 | MG, PRP, BE2 |
| 4 | 615 | 0.76 | 0.82 | 56 | MG, PRP, BE2 |
| 5 | 51 | 0.32 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 958 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 936 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1ZYK · Anthranilate Phosphoribosyltransferase in complex with PRPP, anthranilate and magnesium · the same entry in another collection · chain A against A, TM-score 1.00
- P50384 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (P50384) · a predicted model of the same protein · chain A 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 P50384
- Elsewhere: RCSB PDB 1ZYK · PDBe 1ZYK · UniProt P50384
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