Research workbench
Methylsulfonyl-containing inhibitor bound in the substrate capture site of mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
Analyse Methylsulfonyl-containing inhibitor bound in the substrate capture site of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZOK
- Type
- protein
- Length
- 682 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- A5U4M0
- Ligands
- PRP, 62L, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 342 | 53% helix, 13% strand | A5U4M0 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 340 | 51% helix, 11% strand | A5U4M0 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- 62L · 4-methyl-2-{[2-methyl-6-(methylsulfonyl)phenyl]amino}benzoic acid · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.79 | 0.87 | 51 | MG, PRP, 62L |
| 2 | 552 | 0.76 | 0.84 | 57 | MG, PRP |
| 3 | 63 | 0.34 | 0.77 | 14 | empty |
| 4 | 56 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 813 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4ZOK · Methylsulfonyl-containing inhibitor bound in the substrate capture site of Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- A5U4M0 · AlphaFold monomer V2.0 prediction for anthranilate phosphoribosyltransferase (A5U4M0) · 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 A5U4M0
- Elsewhere: RCSB PDB 4ZOK · PDBe 4ZOK · UniProt A5U4M0
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