MolNFT v1 · #140443 · protein
Structure and function of human serum albumin-metal agent complex
5YB1: “Structure and function of human serum albumin-metal agent complex”. X-ray diffraction, 2 ligands (PLM, 8ZR), 14 pockets (best druggability 0.89). MolNFT v1 #140443 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YB1
- Type
- protein
- Length
- 1,162 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- P02768
- Ligands
- PLM, 8ZR
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serum albumin | protein | 581 | 74% helix, 0% strand | P02768 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 14 copies · chains A, B
- 8ZR · ~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.89 | 0.90 | 115 | PLM |
| 2 | 706 | 0.87 | 0.91 | 80 | PLM |
| 3 | 661 | 0.87 | 0.91 | 72 | PLM |
| 4 | 308 | 0.82 | 0.92 | 38 | PLM |
| 5 | 391 | 0.76 | 0.85 | 36 | PLM, 8ZR |
Interfaces
1 interface between chains.
- A–B · 222 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
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 5YB1 · PDBe 5YB1 · UniProt P02768
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