Research workbench
The crystal structure of trpd (RV2192C) from mycobacterium tuberculosis in complex with prpp and magnesium
Analyse The crystal structure of trpd (RV2192C) from mycobacterium tuberculosis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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