Research workbench
Crystal structure of the N-terminal laglidadg domain of DUF199/WHIA
Analyse Crystal structure of the N-terminal laglidadg domain of DUF199/WHIA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYJ
- Type
- protein
- Length
- 384 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein DUF199/WHIA
- UniProt
- Q9X234
- Ligands
- NA, CL
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein DUF199/WHIA | protein | 186 | 45% helix, 22% strand | Q9X234 |
| D | Protein DUF199/WHIA | protein | 198 | 42% helix, 22% strand | Q9X234 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains D, A
- GOL · Glycerol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.59 | 0.79 | 24 | empty |
| 2 | 138 | 0.53 | 0.81 | 20 | GOL |
| 3 | 83 | 0.47 | 0.81 | 17 | empty |
| 4 | 112 | 0.42 | 0.77 | 17 | CL |
| 5 | 77 | 0.41 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–D · 817 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3HYJ · Crystal structure of the N-terminal LAGLIDADG domain of DUF199/WhiA · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X234 · AlphaFold monomer V2.0 prediction for probable cell division protein whia (Q9X234) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9X234
- Elsewhere: RCSB PDB 3HYJ · PDBe 3HYJ · UniProt Q9X234
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