Research workbench
Crystal structure of a putative glycosyl hydrolase (BDI_1869) from parabacteroides distasonis atcc 8503 at 1.70 a resolution
Analyse Crystal structure of a putative glycosyl hydrolase (BDI_1869) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U1X
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosyl hydrolase
- UniProt
- A6LD40
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative glycosyl hydrolase | protein | 217 | 9% helix, 39% strand | A6LD40 |
| B | Putative glycosyl hydrolase | protein | 223 | 9% helix, 38% strand | A6LD40 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.95 | 14 | empty |
| 2 | 172 | 0.46 | 0.75 | 24 | PGE |
| 3 | 98 | 0.41 | 0.77 | 17 | empty |
| 4 | 109 | 0.36 | 0.74 | 24 | empty |
| 5 | 50 | 0.24 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 848 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3U1X · Crystal structure of a putative glycosyl hydrolase (BDI_1869) from Parabacteroides… · 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 A6LD40
- Elsewhere: RCSB PDB 3U1X · PDBe 3U1X · UniProt A6LD40
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