Research workbench
Lobenzarit-like inhibitor bound in the active site of mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
Analyse Lobenzarit-like inhibitor bound in the active site of mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZOF
- Type
- protein
- Length
- 684 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, 59L, MG, PO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 342 | 53% helix, 13% strand | A5U4M0 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- 59L · 2-[(2-carboxy-5-nitrophenyl)amino]-3-methylbenzoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- IMD · Imidazole · additive · chains A
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 | 484 | 0.77 | 0.85 | 50 | MG, PRP, 59L |
| 2 | 442 | 0.76 | 0.86 | 53 | MG, PRP, 59L |
| 3 | 66 | 0.32 | 0.75 | 15 | empty |
| 4 | 71 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 872 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4ZOF · Lobenzarit-like inhibitor bound in the active site of Mycobacterium tuberculosis… · 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 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 A5U4M0
- Elsewhere: RCSB PDB 4ZOF · PDBe 4ZOF · UniProt A5U4M0
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