Research workbench
OhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium violaceum and reduced by DTT
Analyse OhrB (Organic Hydroperoxide Resistance protein) wild type from Chromobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EBC
- Type
- protein
- Length
- 565 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.87
- Source
- Chromobacterium violaceum
- Molecule
- Organic hydroperoxide resistance protein
- UniProt
- A0A202B6V5
- Ligands
- CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.87 · 3 distinct chains · 32% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Organic hydroperoxide resistance protein | protein | 140 | 33% helix, 32% strand | A0A202B6V5 |
| B | Organic hydroperoxide resistance protein | protein | 143 | 32% helix, 32% strand | A0A202B6V5 |
| D | Organic hydroperoxide resistance protein | protein | 142 | 32% helix, 32% strand | A0A202B6V5 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, C, B, D
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 3 copies · chains B, D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 896 | 0.76 | 0.80 | 87 | CL |
| 2 | 252 | 0.66 | 0.83 | 37 | empty |
| 3 | 305 | 0.65 | 0.81 | 44 | DTT |
| 4 | 217 | 0.65 | 0.83 | 30 | DTT |
| 5 | 272 | 0.64 | 0.81 | 36 | DTT |
Interfaces
6 interfaces between chains.
- B–D · 3371 Ų buried · 71 hydrogen bonds · protein-protein
- A–C · 3147 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 112 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 79 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6EBC · Ohrb (organic hydroperoxide resistance protein) wild type from chromobacterium violaceum… · 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 A0A202B6V5
- Elsewhere: RCSB PDB 6EBC · PDBe 6EBC · UniProt A0A202B6V5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.