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Crystal structure of bacillus subtilis tena Y112F mutant complexed with formyl aminomethyl pyrimidine
Analyse Crystal structure of bacillus subtilis tena Y112F mutant complexed with formyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QCX
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional activator tena
- EC
- 3.5.99.2
- UniProt
- P25052
- Ligands
- PF1
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional activator tena (EC 3.5.99.2) | protein | 222 | 80% helix, 0% strand | P25052 |
| B | Transcriptional activator tena (EC 3.5.99.2) | protein | 227 | 78% helix, 0% strand | P25052 |
Ligands and binding sites
- PF1 · N-[(4-amino-2-methylpyrimidin-5-yl)methyl]-N-(2-hydroxyethyl)formamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.77 | 0.90 | 35 | PF1 |
| 2 | 106 | 0.70 | 0.92 | 23 | PF1 |
| 3 | 299 | 0.64 | 0.80 | 33 | empty |
| 4 | 165 | 0.45 | 0.75 | 25 | empty |
| 5 | 73 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2QCX · Crystal structure of Bacillus subtilis TenA Y112F mutant complexed with formyl… · the same entry in another collection · chain A against A, TM-score 1.00
- P25052 · AlphaFold monomer V2.0 prediction for aminopyrimidine aminohydrolase (P25052) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P25052
- Elsewhere: RCSB PDB 2QCX · PDBe 2QCX · UniProt P25052
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