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Crystal structure of an organic hydroperoxide resistance protein from Elizabethkingia anophelis with crystallant-derived thiocyanate bound
Analyse Crystal structure of an organic hydroperoxide resistance protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9N
- Type
- protein
- Length
- 283 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.2
- Source
- Elizabethkingia anophelis NUHP1
- Molecule
- Organic hydroperoxide resistance protein
- UniProt
- A0A077EDR1
- Ligands
- SCN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · resolution 1.2 · 2 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Organic hydroperoxide resistance protein | protein | 140 | 34% helix, 34% strand | A0A077EDR1 |
| B | Organic hydroperoxide resistance protein | protein | 143 | 33% helix, 32% strand | A0A077EDR1 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, 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 | 138 | 0.68 | 0.89 | 30 | SCN, EDO |
| 2 | 274 | 0.68 | 0.83 | 44 | SCN |
Interfaces
1 interface between chains.
- A–B · 3235 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6D9N · Crystal structure of an organic hydroperoxide resistance protein from elizabethkingia… · 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 A0A077EDR1
- Elsewhere: RCSB PDB 6D9N · PDBe 6D9N · UniProt A0A077EDR1
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