Research workbench
Crystal structure of solute-binding protein related to glycosaminoglycans
Analyse Crystal structure of solute-binding protein related to glycosaminoglycans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GX8
- Type
- protein
- Length
- 946 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein family 1
- UniProt
- D1AWE0
- Ligands
- CA, SO4
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Extracellular solute-binding protein family 1 | protein | 473 | 45% helix, 16% strand | D1AWE0 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- TAR · D(-)-tartaric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.77 | 0.79 | 101 | EDO |
| 2 | 641 | 0.72 | 0.79 | 51 | EDO |
| 3 | 403 | 0.57 | 0.74 | 42 | empty |
| 4 | 361 | 0.56 | 0.75 | 46 | empty |
| 5 | 174 | 0.53 | 0.80 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1743 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5GX8 · Crystal structure of solute-binding protein related to glycosaminoglycans · 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 D1AWE0
- Elsewhere: RCSB PDB 5GX8 · PDBe 5GX8 · UniProt D1AWE0
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