Research workbench
Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1) from desulfitobacterium hafniense dcb-2 at 2.01 a resolution
Analyse Crystal structure of protein with unknown function from DUF364 family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L5O
- Type
- protein
- Length
- 491 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein from DUF364 family
- UniProt
- B8FUJ5
- Ligands
- CL
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein from DUF364 family | protein | 247 | 38% helix, 22% strand | B8FUJ5 |
| B | Uncharacterized protein from DUF364 family | protein | 244 | 41% helix, 23% strand | B8FUJ5 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.77 | 0.83 | 70 | CL, IMD, EDO |
| 2 | 409 | 0.64 | 0.78 | 53 | CL, IMD, EDO |
| 3 | 183 | 0.50 | 0.77 | 26 | empty |
| 4 | 147 | 0.47 | 0.76 | 21 | empty |
| 5 | 125 | 0.43 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 953 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3L5O · Crystal structure of protein with unknown function from DUF364 family (ZP_00559375.1)… · 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 B8FUJ5
- Elsewhere: RCSB PDB 3L5O · PDBe 3L5O · UniProt B8FUJ5
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