Research workbench
Crystal structure of the sheep signalling glycoprotein (sps-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of sps-40
Analyse Crystal structure of the sheep signalling glycoprotein (sps-40) complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PI6
- Type
- protein
- Length
- 361 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3-like protein 1
- UniProt
- Q6TMG6
- Ligands
- MAN, NAG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 361 | 37% helix, 24% strand | Q6TMG6 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- EOH · Ethanol · additive · 3 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.65 | 0.81 | 42 | empty |
| 2 | 354 | 0.61 | 0.77 | 49 | MPD |
| 3 | 70 | 0.34 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2PI6 · Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6TMG6 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (Q6TMG6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6TMG6
- Elsewhere: RCSB PDB 2PI6 · PDBe 2PI6 · UniProt Q6TMG6
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