MolNFT v1 · #36695 · protein
Crystal structure of the ternary complex of signalling glycoprotein frm sheep (sps-40)WITH hexasaccharide (NAG6) and peptide TRP-pro-TRP at 3.0A resolution
2FDM · Chitinase-3-like protein 1: “Crystal structure of the ternary complex of signalling glycoprotein frm sheep (sps-40)WITH hexasaccharide…”. X-ray diffraction, 2 ligands (NAG, NDG), 2 pockets (best druggability 0.75). MolNFT v1 #36695…
- PDB
- 2FDM
- 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; Tripeptide
- UniProt
- Q6TMG6
- Ligands
- NAG, NDG
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitinase-3-like protein 1 | protein | 361 | 36% helix, 24% strand | Q6TMG6 |
| P | Tripeptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.75 | 0.79 | 78 | NDG, NAG |
| 2 | 77 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–P · 139 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2FDM · Crystal structure of the ternary complex of signalling glycoprotein frm sheep… · 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 2FDM · PDBe 2FDM · UniProt Q6TMG6
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