MolNFT v1 · #161574 · protein
Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin and the albumin-biniding side chain of the human growth hormone derivative somapacitan
6QIP: “Ternary complex of fcrn ectodomain, fcrn binding optimised human serum albumin and the albumin-biniding side…”. X-ray diffraction, 2 ligands (HDW, CYS), 16 pockets (best druggability 0.83). MolNFT v1 #161574 on GenesisL1: 3D…
- PDB
- 6QIP
- Type
- protein
- Length
- 949 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin; IgG receptor fcrn large subunit P51; Beta-2-microglobulin
- UniProt
- P02768, P55899, P61769
- Ligands
- HDW, CYS
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 582 | 74% 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, 49% strand | P61769 |
Ligands and binding sites
- HDW · (2~{S})-6-[2-(2-hydroxyethylsulfanyl)ethanoylamino]-2-[2-[2-[2-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(4~{S})-5-oxidanyl-5-oxidanylidene-4-[2-[2-[2-[4-[16-(2~{H}-1,2,3,4-tetrazol-5-yl) hexadecanoylsulfamoyl]butanoylamino]ethoxy]ethoxy]etha noylamino]pentanoyl]amino]pentanoyl]amino]ethoxy]ethox y]ethanoylamino]hexanoic acid · ligand · chains A
- CYS · Cysteine · ligand · chains B, C
- 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
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.83 | 0.88 | 68 | empty |
| 2 | 602 | 0.79 | 0.84 | 49 | empty |
| 3 | 938 | 0.78 | 0.81 | 86 | CYS |
| 4 | 478 | 0.78 | 0.85 | 48 | empty |
| 5 | 120 | 0.74 | 0.93 | 22 | MES |
Interfaces
3 interfaces between chains.
- A–B · 1633 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1528 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 6QIP · 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
- Elsewhere: RCSB PDB 6QIP · PDBe 6QIP · UniProt P02768 · UniProt P55899 · UniProt P61769
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