Research workbench
Crystal structure of equine serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cpa)
Analyse Crystal structure of equine serum albumin in complex with phosphorodithioate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ID9
- Type
- protein
- Length
- 580 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- F7BAY6
- Ligands
- 6A4
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serum albumin | protein | 580 | 74% helix, 0% strand | F7BAY6 |
Ligands and binding sites
- 6A4 · (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate · ligand · chains A
- FMT · Formic acid · additive · 4 copies · chains A
- MLI · Malonate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.79 | 0.85 | 59 | MLI, FMT |
| 2 | 890 | 0.78 | 0.81 | 60 | MLI, FMT |
| 3 | 175 | 0.67 | 0.86 | 32 | empty |
| 4 | 213 | 0.62 | 0.82 | 25 | FMT |
| 5 | 230 | 0.62 | 0.81 | 27 | 6A4 |
Modifications
Observed in the structure: 17 disulfide (disulfide).
Compared structures
- 5ID9 · Crystal structure of equine serum albumin in complex with phosphorodithioate derivative… · the same entry in another collection · chain A against A, TM-score 1.00
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 F7BAY6
- Elsewhere: RCSB PDB 5ID9 · PDBe 5ID9 · UniProt F7BAY6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.