Research workbench
OXYR2 E204G regulatory domain from vibrio vulnificus
Analyse OXYR2 E204G regulatory domain from vibrio vulnificus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B70
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr family transcriptional regulator
- UniProt
- A0A087I947
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysr family transcriptional regulator | protein | 209 | 33% helix, 27% strand | A0A087I947 |
| B | Lysr family transcriptional regulator | protein | 214 | 31% helix, 29% strand | A0A087I947 |
| C | Lysr family transcriptional regulator | protein | 211 | 33% helix, 27% strand | A0A087I947 |
| D | Lysr family transcriptional regulator | protein | 214 | 31% helix, 26% strand | A0A087I947 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.75 | 0.79 | 69 | empty |
| 2 | 247 | 0.62 | 0.81 | 27 | empty |
| 3 | 116 | 0.59 | 0.86 | 25 | empty |
| 4 | 160 | 0.55 | 0.81 | 32 | empty |
| 5 | 60 | 0.31 | 0.75 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1812 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1812 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 326 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 130 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5B70 · OxyR2 E204G regulatory domain from Vibrio vulnificus · 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 A0A087I947
- Elsewhere: RCSB PDB 5B70 · PDBe 5B70 · UniProt A0A087I947
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