Research workbench
The crystal structure of a degv family protein from eubacterium eligens loaded with heptadecanoic acid to 1.80 ångström resolution (alternative refinement of pdb 3FDJ with heptadecanoic acid)
Analyse The crystal structure of a degv family protein from eubacterium eligens loaded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UXY
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Degv family protein
- UniProt
- D0VX07
- Ligands
- X90, NA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Degv family protein | protein | 276 | 40% helix, 25% strand | D0VX07 |
Ligands and binding sites
- X90 · heptadecanoic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.79 | 0.95 | 30 | X90 |
| 2 | 88 | 0.40 | 0.78 | 16 | empty |
| 3 | 59 | 0.32 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 5UXY · The crystal structure of a DegV family protein from Eubacterium eligens loaded with… · 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 D0VX07
- Elsewhere: RCSB PDB 5UXY · PDBe 5UXY · UniProt D0VX07
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