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Crystal structure of plasma-derived human serum albumin
Analyse Crystal structure of plasma-derived 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
- 5Z0B
- Type
- protein
- Length
- 1,694 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- P02768
- Ligands
- OCA, PLM, EIC, TRP, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serum albumin | protein | 581 | 74% helix, 0% strand | P02768 |
| C | Serum albumin | protein | 532 | 73% helix, 0% strand | P02768 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 5 copies · chains A, B, C
- PLM · Palmitic acid · ligand · 4 copies · chains A, B, C
- EIC · Linoleic acid · ligand · 3 copies · chains A, B, C
- TRP · Tryptophan · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 13 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, C, B
- 1PE · Pentaethylene glycol · additive · chains B
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 | 670 | 0.84 | 0.88 | 57 | EIC, SO4 |
| 2 | 571 | 0.83 | 0.88 | 47 | EIC, SO4 |
| 3 | 787 | 0.83 | 0.85 | 61 | EIC, SO4 |
| 4 | 543 | 0.80 | 0.86 | 51 | PLM, PEG |
| 5 | 699 | 0.80 | 0.84 | 61 | PLM, SO4, PEG |
Interfaces
3 interfaces between chains.
- A–C · 471 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 284 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 283 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 disulfide, 3 modified (disulfide, oxidation).
Compared structures
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
- Elsewhere: RCSB PDB 5Z0B · PDBe 5Z0B · UniProt P02768
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