Research workbench
Crystal structure of mouse serum amyloid A3 (SAA3) bound with retinol
Analyse Crystal structure of mouse serum amyloid A3 (SAA3) bound with retinol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PY0
- Type
- protein
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum amyloid a-3 protein
- UniProt
- P04918
- Ligands
- RTL
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum amyloid a-3 protein | protein | 101 | 73% helix, 0% strand | P04918 |
| B | Serum amyloid a-3 protein | protein | 100 | 74% helix, 0% strand | P04918 |
| C | Serum amyloid a-3 protein | protein | 98 | 72% helix, 0% strand | P04918 |
Ligands and binding sites
- RTL · Retinol · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.81 | 0.82 | 75 | RTL |
| 2 | 109 | 0.40 | 0.75 | 13 | empty |
| 3 | 52 | 0.27 | 0.74 | 9 | empty |
Interfaces
3 interfaces between chains.
- A–B · 441 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 334 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 297 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PY0 · Crystal Structure of mouse Serum Amyloid A3 (SAA3) bound with Retinol · the same entry in another collection · chain A against A, TM-score 1.00
- P04918 · AlphaFold monomer V2.0 prediction for serum amyloid a-3 protein (P04918) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P04918
- Elsewhere: RCSB PDB 6PY0 · PDBe 6PY0 · UniProt P04918
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