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Pyrr, the regulator of the pyrimidine biosynthetic operon in bacillus caldolyticus, nucleotide-bound form
Analyse Pyrr, the regulator of the pyrimidine biosynthetic operon in bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XZ8
- Type
- protein
- Length
- 323 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrr bifunctional protein
- EC
- 2.4.2.9
- UniProt
- P41007
- Ligands
- 5GP, 3GP, U5P, MG
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrr bifunctional protein (EC 2.4.2.9) | protein | 162 | 33% helix, 31% strand | P41007 |
| B | Pyrr bifunctional protein (EC 2.4.2.9) | protein | 161 | 34% helix, 32% strand | P41007 |
Ligands and binding sites
- 5GP · Guanosine-5'-monophosphate · ligand · chains A
- 3GP · Guanosine-3'-monophosphate · ligand · chains A
- U5P · Uridine-5'-monophosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 147 | 0.43 | 0.75 | 22 | MG, 5GP |
| 2 | 122 | 0.40 | 0.75 | 24 | MG, U5P |
| 3 | 116 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1XZ8 · Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus… · the same entry in another collection · chain A against A, TM-score 1.00
- P41007 · AlphaFold monomer V2.0 prediction for bifunctional protein pyrr (P41007) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P41007
- Elsewhere: RCSB PDB 1XZ8 · PDBe 1XZ8 · UniProt P41007
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