MolNFT v1 · #32693 · protein
Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection
2BY1 · Maltooligosyltrehalose trehalohydrolase: “Is radiation damage dependent on the dose-rate used during macromolecular crystallography data collection”. X-ray diffraction, 2 ligands (GLC, MG), 4 pockets (best druggability 0.64). MolNFT…
- PDB
- 2BY1
- Type
- protein
- Length
- 580 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltooligosyltrehalose trehalohydrolase
- EC
- 3.2.1.1
- UniProt
- Q9RX51
- Ligands
- GLC, MG
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltooligosyltrehalose trehalohydrolase (EC 3.2.1.1) | protein | 580 | 32% helix, 23% strand | Q9RX51 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
- MG · Magnesium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- BME · Beta-mercaptoethanol · additive · 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 | 511 | 0.64 | 0.76 | 55 | GLC |
| 2 | 101 | 0.56 | 0.85 | 19 | empty |
| 3 | 79 | 0.34 | 0.75 | 13 | empty |
| 4 | 60 | 0.32 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 8 modified, 1 covalent (engineered, additive adduct).
Compared structures
- 2BY1 · Is radiation damage dependent on the dose-rate used during macromolecular crystallography… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RX51 · AlphaFold monomer V2.0 prediction for malto-oligosyltrehalose trehalohydrolase (Q9RX51) · a predicted model of the same protein · chain A 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 Q9RX51
- Elsewhere: RCSB PDB 2BY1 · PDBe 2BY1 · UniProt Q9RX51
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