Research workbench
Crystal structure of cupin 2 domain-containing protein HHAL_0468 from halorhodospira halophila
Analyse Crystal structure of cupin 2 domain-containing protein HHAL_0468 from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IBM
- Type
- protein
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cupin 2, conserved barrel domain protein
- UniProt
- A1WU94
- Ligands
- ZN, K
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cupin 2, conserved barrel domain protein | protein | 145 | 9% helix, 43% strand | A1WU94 |
| B | Cupin 2, conserved barrel domain protein | protein | 146 | 11% helix, 40% strand | A1WU94 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.58 | 0.79 | 35 | empty |
| 2 | 155 | 0.52 | 0.79 | 23 | GOL |
Interfaces
1 interface between chains.
- A–B · 1875 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3IBM · CRYSTAL STRUCTURE OF cupin 2 domain-containing protein Hhal_0468 FROM Halorhodospira… · 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 A1WU94
- Elsewhere: RCSB PDB 3IBM · PDBe 3IBM · UniProt A1WU94
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