Research workbench
Anthranilate phosphoribosyltransferase (trpd) from mycobacterium tuberculosis (complex with inhibitor ACS172)
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
- 3QQS
- Type
- protein
- Length
- 1,365 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anthranilate phosphoribosyltransferase
- EC
- 2.4.2.18
- UniProt
- P66992
- Ligands
- 17C, PRP, DPO, MG
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 346 | 51% helix, 12% strand | P66992 |
| C | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 343 | 51% helix, 13% strand | P66992 |
| D | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 330 | 53% helix, 12% strand | P66992 |
Ligands and binding sites
- 17C · 2,2'-iminodibenzoic acid · ligand · 7 copies · chains A, B, C, D
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · 3 copies · chains A, B, C
- DPO · Diphosphate · ligand · chains D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.81 | 0.83 | 94 | PRP, MG, 17C |
| 2 | 438 | 0.79 | 0.88 | 55 | PRP, MG, 17C |
| 3 | 604 | 0.78 | 0.84 | 55 | PRP, MG, 17C |
| 4 | 489 | 0.67 | 0.78 | 47 | DPO, 17C |
| 5 | 129 | 0.42 | 0.75 | 23 | empty |
Interfaces
5 interfaces between chains.
- B–D · 878 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3QQS · 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 3QQS · PDBe 3QQS · UniProt P66992
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