Research workbench
Crystal structure of human 5T4 (wnt-activated inhibitory factor 1, trophoblast glycoprotein)
Analyse Crystal structure of human 5T4 (wnt-activated inhibitory factor 1, trophoblast… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CNC
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trophoblast glycoprotein
- UniProt
- Q13641
- Ligands
- NAG, NA, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trophoblast glycoprotein | protein | 274 | 19% helix, 18% strand | Q13641 |
| B | Trophoblast glycoprotein | protein | 278 | 19% helix, 17% strand | Q13641 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.69 | 0.96 | 19 | empty |
| 2 | 72 | 0.41 | 0.80 | 21 | PEG |
| 3 | 78 | 0.29 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 95 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4CNC · Crystal structure of human 5T4 (Wnt-activated inhibitory factor 1, Trophoblast… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13641 · AlphaFold monomer V2.0 prediction for trophoblast glycoprotein (Q13641) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q13641
- Elsewhere: RCSB PDB 4CNC · PDBe 4CNC · UniProt Q13641
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