Research workbench
Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and fv anti beta subunit
Analyse Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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