Research workbench
Ohrb (organic hydroperoxide resistance protein) mutant (C60A) from chromobacterium violaceum, interacting with dihydrolipoamide
Analyse Ohrb (organic hydroperoxide resistance protein) mutant (C60A) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EBD
- Type
- protein
- Length
- 563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Organic hydroperoxide resistance protein
- UniProt
- A0A202B6V5
- Ligands
- J3S, CL
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Organic hydroperoxide resistance protein | protein | 140 | 33% helix, 31% strand | A0A202B6V5 |
| C | Organic hydroperoxide resistance protein | protein | 143 | 32% helix, 31% strand | A0A202B6V5 |
Ligands and binding sites
- J3S · (6S)-6,8-disulfanyloctanamide · ligand · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · 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 | 361 | 0.68 | 0.81 | 39 | J3S |
| 2 | 295 | 0.67 | 0.82 | 31 | empty |
| 3 | 65 | 0.67 | 0.95 | 30 | empty |
| 4 | 411 | 0.66 | 0.79 | 50 | J3S |
| 5 | 296 | 0.66 | 0.81 | 29 | J3S |
Interfaces
5 interfaces between chains.
- C–D · 3180 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 3101 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 207 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 204 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 186 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EBD · OhrB (Organic Hydroperoxide Resistance protein) mutant (C60A) from Chromobacterium… · 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 6EBD · PDBe 6EBD · UniProt A0A202B6V5
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