Research workbench
Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 2.9A resolution
Analyse Crystal structure of the complex formed between goat signalling protein with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DT2
- 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
- Q8SPQ0
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 361 | 36% helix, 24% strand | Q8SPQ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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 | 474 | 0.70 | 0.80 | 58 | NAG |
| 2 | 201 | 0.53 | 0.78 | 26 | empty |
| 3 | 52 | 0.31 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2DT2 · Crystal structure of the complex formed between goat signalling protein with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SPQ0 · AlphaFold monomer V2.0 prediction for chitinase-3-like protein 1 (Q8SPQ0) · 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 Q8SPQ0
- Elsewhere: RCSB PDB 2DT2 · PDBe 2DT2 · UniProt Q8SPQ0
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