Research workbench
The crystal structure of a protein disulfide oxidoreductase from aeropyrum pernix K1
Analyse The crystal structure of a protein disulfide oxidoreductase from aeropyrum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HLS
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein disulfide oxidoreductase
- UniProt
- Q9YDZ4
- Ligands
- CL
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein disulfide oxidoreductase | protein | 232 | 38% helix, 21% strand | Q9YDZ4 |
| B | Protein disulfide oxidoreductase | protein | 229 | 39% helix, 21% strand | Q9YDZ4 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.55 | 0.78 | 28 | empty |
| 2 | 66 | 0.34 | 0.76 | 18 | empty |
| 3 | 86 | 0.34 | 0.74 | 22 | empty |
| 4 | 83 | 0.32 | 0.74 | 21 | empty |
| 5 | 53 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2HLS · The crystal structure of a protein disulfide oxidoreductase from Aeropyrum pernix k1 · 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 Q9YDZ4
- Elsewhere: RCSB PDB 2HLS · PDBe 2HLS · UniProt Q9YDZ4
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