MolNFT v1 · #19281 · protein
Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and fv anti beta subunit
1QFW · Gonadotropin alpha subunit: “Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and fv anti beta subunit”. X-ray diffraction, 1 ligand (NAG), 8 pockets (best druggability 0.74). MolNFT v1 #19281 on GenesisL1…
- PDB
- 1QFW
- Type
- protein
- Length
- 646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gonadotropin alpha subunit; Gonadotrophin beta subunit; Antibody (anti alpha subunit)…
- UniProt
- P01215, P01233
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 2% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gonadotropin alpha subunit | protein | 87 | 5% helix, 57% strand | P01215 |
| B | Gonadotrophin beta subunit | protein | 110 | 0% helix, 48% strand | P01233 |
| L | Antibody (anti alpha subunit) (light chain) | protein | 111 | 0% helix, 41% strand | — |
| H | Antibody (anti alpha subunit) (heavy chain) | protein | 111 | 3% helix, 33% strand | — |
| M | Antibody (anti beta subunit) (light chain) | protein | 107 | 0% helix, 42% strand | — |
| I | Antibody (anti beta subunit) (heavy chain) | protein | 120 | 5% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.74 | 0.85 | 56 | NAG |
| 2 | 81 | 0.46 | 0.81 | 15 | empty |
| 3 | 149 | 0.44 | 0.75 | 22 | empty |
| 4 | 100 | 0.41 | 0.77 | 20 | empty |
| 5 | 99 | 0.40 | 0.77 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2260 Ų buried · 33 hydrogen bonds · protein-protein
- M–I · 917 Ų buried · 7 hydrogen bonds · protein-protein
- L–H · 786 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 482 Ų buried · 8 hydrogen bonds · protein-protein
- B–M · 413 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1QFW · Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and fv anti… · the same entry in another collection · chain L against L, TM-score 1.00
- P01215 · AlphaFold monomer V2.0 prediction for glycoprotein hormones alpha chain (P01215) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P01215
- Every structure of UniProt P01233
- Elsewhere: RCSB PDB 1QFW · PDBe 1QFW · UniProt P01215 · UniProt P01233
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