MolNFT v1 · #141360 · protein
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
5Z4V · Chitinase-3-like protein 1: “Crystal structure of the sheep signalling glycoprotein (sps-40) complex with 2-methyl-2-4-pentanediol at…”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.62). MolNFT v1 #141360 on…
- PDB
- 5Z4V
- 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
- NAG
- Pockets
- 5 · best druggability 0.62
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.62 | 0.85 | 27 | empty |
| 2 | 268 | 0.60 | 0.79 | 30 | MPD |
| 3 | 110 | 0.38 | 0.75 | 18 | empty |
| 4 | 52 | 0.31 | 0.76 | 15 | empty |
| 5 | 52 | 0.30 | 0.76 | 12 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5Z4V · 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 5Z4V · PDBe 5Z4V · UniProt Q6TMG6
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