Research workbench
The structure of a reduced form of oxyr from N. meningitidis
Analyse The structure of a reduced form of oxyr from N. meningitidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JV9
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, lysr family
- UniProt
- Q9K1H8
- Ligands
- CL
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator, lysr family | protein | 216 | 32% helix, 27% strand | Q9K1H8 |
| B | Transcriptional regulator, lysr family | protein | 204 | 33% helix, 29% strand | Q9K1H8 |
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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 954 | 0.76 | 0.78 | 59 | CL |
| 2 | 105 | 0.44 | 0.78 | 20 | empty |
| 3 | 56 | 0.44 | 0.83 | 14 | empty |
| 4 | 85 | 0.38 | 0.76 | 20 | empty |
| 5 | 69 | 0.33 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1132 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3JV9 · The structure of a reduced form of OxyR from N. meningitidis · 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 Q9K1H8
- Elsewhere: RCSB PDB 3JV9 · PDBe 3JV9 · UniProt Q9K1H8
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