Research workbench
Ohrb (organic hydroperoxide resistance protein) from chromobacterium violaceum
Analyse Ohrb (organic hydroperoxide resistance protein) from chromobacterium violaceum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EB4
- Type
- protein
- Length
- 561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Organic hydroperoxide resistance protein
- UniProt
- A0A202B6V5
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Organic hydroperoxide resistance protein | protein | 141 | 33% helix, 33% strand | A0A202B6V5 |
| B, C, D | Organic hydroperoxide resistance protein | protein | 140 | 33% helix, 33% strand | A0A202B6V5 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, D
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 | 396 | 0.68 | 0.81 | 50 | PEG |
| 2 | 284 | 0.67 | 0.82 | 32 | PEG |
| 3 | 294 | 0.67 | 0.82 | 31 | PEG |
| 4 | 56 | 0.67 | 0.96 | 28 | empty |
| 5 | 384 | 0.66 | 0.79 | 46 | PEG |
Interfaces
5 interfaces between chains.
- A–B · 3189 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3162 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 189 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 182 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EB4 · OhrB (Organic Hydroperoxide Resistance protein) 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 6EB4 · PDBe 6EB4 · UniProt A0A202B6V5
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