MolNFT v1 · #120256 · protein
Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin disaccharide
5GUB · Extracellular solute-binding protein family 1: “Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated chondroitin…”. X-ray diffraction, 3 ligands (GCD, NGA, CA), 12 pockets (best druggability…
- PDB
- 5GUB
- Type
- protein
- Length
- 1,418 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein family 1
- UniProt
- D1AWE0
- Ligands
- GCD, NGA, CA
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein family 1 | protein | 474 | 46% helix, 17% strand | D1AWE0 |
| B | Extracellular solute-binding protein family 1 | protein | 471 | 47% helix, 17% strand | D1AWE0 |
| C | Extracellular solute-binding protein family 1 | protein | 473 | 45% helix, 17% strand | D1AWE0 |
Ligands and binding sites
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 3 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.88 | 0.89 | 128 | NGA, GCD, MES, EDO |
| 2 | 1156 | 0.86 | 0.87 | 94 | NGA, GCD |
| 3 | 1113 | 0.86 | 0.87 | 105 | NGA, GCD |
| 4 | 325 | 0.75 | 0.87 | 43 | empty |
| 5 | 175 | 0.62 | 0.84 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–B · 979 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5GUB · Crystal structure of solute-binding protein complexed with sulfate group-free unsaturated… · 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 5GUB · PDBe 5GUB · UniProt D1AWE0
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