Research workbench
Structure of the pgab (bpsb) glycoside hydrolase domain from bordetella bronchiseptica
Analyse Structure of the pgab (bpsb) glycoside hydrolase domain from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AU1
- Type
- protein
- Length
- 706 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hemin storage protein
- EC
- 3.2.1.-
- UniProt
- A0A0H3LKK6
- Ligands
- SO4, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative hemin storage protein (EC 3.2.1.-) | protein | 353 | 43% helix, 16% strand | A0A0H3LKK6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.79 | 0.80 | 78 | EDO |
| 2 | 1057 | 0.73 | 0.76 | 82 | SO4 |
| 3 | 125 | 0.48 | 0.79 | 24 | empty |
| 4 | 88 | 0.44 | 0.80 | 21 | empty |
| 5 | 51 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6AU1 · Structure of the PgaB (BpsB) glycoside hydrolase domain from Bordetella bronchiseptica · 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 A0A0H3LKK6
- Elsewhere: RCSB PDB 6AU1 · PDBe 6AU1 · UniProt A0A0H3LKK6
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