Research workbench
Bordetella pertussis globin coupled sensor regulatory domain (bpegreg)
Analyse Bordetella pertussis globin coupled sensor regulatory domain (bpegreg) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M9A
- Type
- protein
- Length
- 469 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signaling protein
- EC
- 2.7.7.65
- UniProt
- A0A131IFY0
- Ligands
- HEM, PEO, CA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Signaling protein (EC 2.7.7.65) | protein | 156 | 85% helix, 0% strand | A0A131IFY0 |
| C | Signaling protein (EC 2.7.7.65) | protein | 157 | 85% helix, 0% strand | A0A131IFY0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.73 | 0.86 | 28 | HEM |
| 2 | 268 | 0.73 | 0.86 | 30 | HEM, PEO |
| 3 | 265 | 0.72 | 0.85 | 26 | HEM, PEO |
| 4 | 271 | 0.52 | 0.75 | 31 | empty |
| 5 | 167 | 0.44 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 269 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 256 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6M9A · Bordetella pertussis globin coupled sensor regulatory domain (BpeGReg) · 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 A0A131IFY0
- Elsewhere: RCSB PDB 6M9A · PDBe 6M9A · UniProt A0A131IFY0
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