Research workbench
Crystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cpa)
Analyse Crystal structure of human 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
- 5ID7
- Type
- protein
- Length
- 1,164 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serum albumin
- UniProt
- P02768
- Ligands
- 6A4
- Pockets
- 15 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serum albumin | protein | 582 | 75% helix, 0% strand | P02768 |
Ligands and binding sites
- 6A4 · (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate · ligand · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.91 | 0.92 | 121 | 6A4, PGE, PEG |
| 2 | 1156 | 0.88 | 0.89 | 104 | 6A4 |
| 3 | 420 | 0.82 | 0.90 | 57 | empty |
| 4 | 563 | 0.78 | 0.84 | 61 | PGE |
| 5 | 251 | 0.76 | 0.89 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
- 5ID7 · Crystal structure of human serum albumin in complex with phosphorodithioate derivative of… · the same entry in another collection · chain A against A, TM-score 1.00
- P02768 · AlphaFold monomer V2.0 prediction for albumin (P02768) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 5ID7 · PDBe 5ID7 · UniProt P02768
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