Research workbench
Bianthranilate-like inhibitor with 4-atom "line" and phosphonate "hook" fishing for hydrogen bond donors in mycobacterium tuberculosis anthranilate phosphoribosyltransferase (anprt; trpd)
Analyse Bianthranilate-like inhibitor with 4-atom "line" and phosphonate "hook" fishing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BO2
- Type
- protein
- Length
- 667 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
- 7P1
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 331 | 56% helix, 12% strand | A5U4M0 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 336 | 54% helix, 12% strand | A5U4M0 |
Ligands and binding sites
- 7P1 · 2-[(2-carboxyphenyl)amino]-5-(3-phosphonopropoxy)benzoic acid · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 5 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 | 410 | 0.70 | 0.82 | 43 | 7P1, IMD |
| 2 | 395 | 0.64 | 0.79 | 38 | 7P1 |
| 3 | 88 | 0.35 | 0.75 | 21 | empty |
| 4 | 50 | 0.33 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5BO2 · Bianthranilate-like inhibitor with 4-atom line" and phosphonate "hook" fishing for… · 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 5BO2 · PDBe 5BO2 · UniProt A5U4M0
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