MolNFT v1 · #29543 · protein
Crystal structure of the goat signalling protein (spg-40) complexed with a designed peptide TRP-pro-TRP at 3.2A resolution
1ZBV · Chitinase-3 like protein 1: “Crystal structure of the goat signalling protein (spg-40) complexed with a designed peptide TRP-pro-TRP at…”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.67). MolNFT v1 #29543 on…
- PDB
- 1ZBV
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitinase-3 like protein 1; Wpw
- UniProt
- Q8SPQ0
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3 like protein 1 | protein | 361 | 35% helix, 22% strand | Q8SPQ0 |
| B | Wpw | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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 | 492 | 0.67 | 0.78 | 54 | empty |
| 2 | 140 | 0.62 | 0.85 | 30 | empty |
| 3 | 59 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 238 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1ZBV · Crystal Structure of the goat signalling protein (SPG-40) complexed with a designed… · 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 1ZBV · PDBe 1ZBV · UniProt Q8SPQ0
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