Research workbench
Crystal structure of a high affinity human serum albumin variant bound to the neonatal Fc receptor
Analyse Crystal structure of a high affinity human serum albumin variant bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K71
- Type
- protein
- Length
- 1,888 residues
- Chains
- 6
- 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
- SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 583 | 73% helix, 0% strand | P02768 |
| B, E | IgG receptor fcrn large subunit P51 | protein | 264 | 27% helix, 44% strand | P55899 |
| C, F | Beta-2-microglobulin | protein | 99 | 0% helix, 49% strand | P61769 |
| D | Serum albumin | protein | 579 | 72% helix, 0% strand | P02768 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.86 | 0.87 | 129 | SO4 |
| 2 | 441 | 0.82 | 0.90 | 64 | SO4 |
| 3 | 1026 | 0.80 | 0.82 | 98 | empty |
| 4 | 1098 | 0.80 | 0.81 | 104 | SO4 |
| 5 | 389 | 0.79 | 0.88 | 49 | SO4 |
Interfaces
7 interfaces between chains.
- A–B · 1721 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1651 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1482 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1482 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 944 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 4K71 · Crystal structure of a high affinity Human Serum Albumin variant bound to the Neonatal Fc… · the same entry in another collection · chain C against C, 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 E 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 F against A, TM-score 0.98
- 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 4K71 · PDBe 4K71 · UniProt P02768 · UniProt P55899 · UniProt P61769
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