Research workbench
Anthranilate phosphoribosyltransferase (trpd) from mycobacterium tuberculosis (complex with inhibitor ACS145)
Analyse Anthranilate phosphoribosyltransferase (trpd) from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R88
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P66992
- Ligands
- PRP, 14F, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 344 | 52% helix, 13% strand | P66992 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 2 copies · chains A, B
- 14F · 2-amino-4,5-dimethoxybenzoic acid · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · 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 | 512 | 0.79 | 0.86 | 51 | PRP, MG, 14F |
| 2 | 443 | 0.78 | 0.87 | 50 | PRP, MG |
| 3 | 77 | 0.34 | 0.75 | 17 | empty |
| 4 | 70 | 0.30 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 878 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3R88 · Anthranilate phosphoribosyltransferase (trpD) from Mycobacterium tuberculosis (complex… · 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 P66992
- Elsewhere: RCSB PDB 3R88 · PDBe 3R88 · UniProt P66992
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