Research workbench
Crystal structure of solute-binding protein complexed with unsaturated chondroitin disaccharide with two sulfate groups at C-4 and C-6 positions of galnac
Analyse Crystal structure of solute-binding protein complexed with unsaturated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XS8
- Type
- protein
- Length
- 1,896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein family 1
- UniProt
- D1AWE0
- Ligands
- 8EX, GCD, CA
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Extracellular solute-binding protein family 1 | protein | 474 | 46% helix, 17% strand | D1AWE0 |
Ligands and binding sites
- 8EX · 2-acetamido-2-deoxy-4,6-di-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains A, B, C, D
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.85 | 0.86 | 80 | 8EX, GCD |
| 2 | 956 | 0.85 | 0.86 | 79 | 8EX, GCD |
| 3 | 973 | 0.85 | 0.86 | 79 | 8EX, GCD |
| 4 | 1199 | 0.84 | 0.85 | 85 | 8EX, GCD |
| 5 | 376 | 0.66 | 0.80 | 48 | empty |
Interfaces
3 interfaces between chains.
- B–D · 871 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 843 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 163 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5XS8 · Crystal structure of solute-binding protein complexed with unsaturated chondroitin… · 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 5XS8 · PDBe 5XS8 · UniProt D1AWE0
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