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Crystal structure of pyrr, the regulator of the pyrimidine biosynthetic operon in bacillus caldolyticus, ump-bound form
Analyse Crystal structure of pyrr, the regulator of the pyrimidine biosynthetic operon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IGB
- Type
- protein
- Length
- 345 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
- U5P
- Pockets
- 4 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrr bifunctional protein (EC 2.4.2.9) | protein | 172 | 31% helix, 38% strand | P41007 |
| B | Pyrr bifunctional protein (EC 2.4.2.9) | protein | 173 | 32% helix, 37% strand | P41007 |
Ligands and binding sites
- U5P · Uridine-5'-monophosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.50 | 0.75 | 28 | U5P |
| 2 | 149 | 0.44 | 0.75 | 25 | U5P |
| 3 | 135 | 0.39 | 0.74 | 22 | empty |
| 4 | 67 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 576 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2IGB · Crystal Structure of PyrR, The Regulator Of The Pyrimidine Biosynthetic Operon In… · 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 A against A, TM-score 0.98
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 2IGB · PDBe 2IGB · UniProt P41007
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