Research workbench
Brucella periplasmic binding protein yehz
Analyse Brucella periplasmic binding protein yehz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TEU
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substrate-binding region of ABC-type glycine betaine transport system
- UniProt
- Q2YP76
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substrate-binding region of ABC-type glycine betaine transport system | protein | 294 | 46% helix, 18% strand | Q2YP76 |
| B | Substrate-binding region of ABC-type glycine betaine transport system | protein | 295 | 46% helix, 17% strand | Q2YP76 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.71 | 0.77 | 94 | SO4 |
| 2 | 62 | 0.46 | 0.84 | 17 | TLA |
| 3 | 95 | 0.43 | 0.79 | 21 | TLA |
| 4 | 50 | 0.25 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 654 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TEU · Brucella periplasmic binding protein YehZ · 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 Q2YP76
- Elsewhere: RCSB PDB 5TEU · PDBe 5TEU · UniProt Q2YP76
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