Research workbench
Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin and the human growth hormone derivative somapacitan
Analyse Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QIO
- Type
- protein
- Length
- 951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin; IgG receptor fcrn large subunit P51; Beta-2-microglobulin; Somatotropin
- UniProt
- P02768, P55899, P61769, P01241
- Ligands
- CYS, JG5
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 583 | 73% helix, 0% strand | P02768 |
| B | IgG receptor fcrn large subunit P51 | protein | 267 | 25% helix, 42% strand | P55899 |
| C | Beta-2-microglobulin | protein | 100 | 0% helix, 50% strand | P61769 |
| D | Somatotropin | protein | 1 | 0% helix, 0% strand | P01241 |
Ligands and binding sites
- CYS · Cysteine · ligand · chains B, C
- JG5 · (2S)-6-acetamido-2-[[2-[2-[2-[[4-carboxy-4-[[(4S)-4-carboxy-4-[[2-[2-[2-[4-[16-(1H-tetrazol-5-yl) hexadecanoylsulfamoyl]butanoylamino]ethoxy]ethoxy]acet yl]amino]butanoyl]amino]butanoyl]amino]ethoxy]ethoxy]a cetyl]amino]hexanoic acid · ligand · chains A, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.83 | 0.87 | 75 | empty |
| 2 | 828 | 0.81 | 0.84 | 95 | empty |
| 3 | 601 | 0.78 | 0.84 | 54 | empty |
| 4 | 956 | 0.78 | 0.80 | 95 | CYS |
| 5 | 97 | 0.70 | 0.92 | 22 | MES |
Interfaces
3 interfaces between chains.
- A–B · 1680 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1573 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6QIO · Ternary complex of FcRn ectodomain, FcRn binding optimised human serum albumin and the… · the same entry in another collection · chain A against A, TM-score 1.00
- P55899 · AlphaFold monomer V2.0 prediction for IgG receptor fcrn large subunit P51 (P55899) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · 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 P02768
- Every structure of UniProt P55899
- Every structure of UniProt P61769
- Every structure of UniProt P01241
- Elsewhere: RCSB PDB 6QIO · PDBe 6QIO · UniProt P02768 · UniProt P55899 · UniProt P61769 · UniProt P01241
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