MolNFT v1 · #30182 · protein
The crystal structure of trpd (RV2192C) from mycobacterium tuberculosis in complex with prpp and magnesium
1ZVW · Anthranilate phosphoribosyltransferase: “The crystal structure of trpd (RV2192C) from mycobacterium tuberculosis in complex with prpp and magnesium”. X-ray diffraction, 3 ligands (PRP, BEN, MG), 4 pockets (best druggability 0.77).…
- PDB
- 1ZVW
- Type
- protein
- Length
- 679 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, BEN, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 346 | 51% helix, 12% strand | P66992 |
| B | Anthranilate phosphoribosyltransferase (EC 2.4.2.18) | protein | 333 | 50% helix, 13% strand | P66992 |
Ligands and binding sites
- PRP · 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose · ligand · chains A
- BEN · Benzamidine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · 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 | 635 | 0.77 | 0.83 | 59 | MG, PRP |
| 2 | 550 | 0.67 | 0.77 | 61 | empty |
| 3 | 53 | 0.40 | 0.82 | 18 | empty |
| 4 | 50 | 0.39 | 0.81 | 16 | empty |
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1ZVW · The Crystal Structure of TrpD (Rv2192c) from Mycobacterium tuberculosis in Complex with… · 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 1ZVW · PDBe 1ZVW · UniProt P66992
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