Research workbench
Crystal Structure of the putative amino acid-binding periplasmic ABC transporter protein from Candidatus Liberibacter asiaticus in complex with Cysteine
Analyse Crystal Structure of the putative amino acid-binding periplasmic ABC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6A8S
- Type
- protein
- Length
- 468 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.05
- Source
- Liberibacter asiaticus (strain psy62)
- Molecule
- Putative amino acid-binding periplasmic ABC transporter protein
- UniProt
- C6XGT2
- Ligands
- CYS, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.05 · 1 distinct chain · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative amino acid-binding periplasmic ABC transporter protein | protein | 234 | 40% helix, 28% strand | C6XGT2 |
Ligands and binding sites
- CYS · Cysteine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 439 | 0.80 | 0.87 | 51 | EDO, CYS |
| 2 | 423 | 0.79 | 0.88 | 50 | EDO, CYS |
| 3 | 112 | 0.78 | 0.97 | 24 | empty |
| 4 | 62 | 0.73 | 0.98 | 28 | empty |
| 5 | 213 | 0.48 | 0.75 | 32 | EDO |
Interfaces
1 interface between chains.
- A–B · 1288 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6A8S · Crystal structure of the putative amino acid-binding periplasmic ABC transporter protein… · 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 C6XGT2
- Elsewhere: RCSB PDB 6A8S · PDBe 6A8S · UniProt C6XGT2
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