MolNFT v1 · #161573 · protein
Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin and the human growth hormone derivative somapacitan
6QIO: “Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin and the human growth hormone…”. X-ray diffraction, 2 ligands (CYS, JG5), 10 pockets (best druggability 0.83). MolNFT v1 #161573 on GenesisL1: 3D…
- 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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