MolNFT v1 · #122031 · protein
Crystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic phosphatidic acid (cpa)
5ID7: “Crystal structure of human serum albumin in complex with phosphorodithioate derivative of myristoyl cyclic…”. X-ray diffraction, 1 ligand (6A4), 15 pockets (best druggability 0.91). MolNFT v1 #122031 on GenesisL1: 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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