MolNFT v1 · #191205 · protein
The S variant of human ALPHA1-antitrypsin, structure and implications for function and metabolism
8API · Alpha-1 antitrypsin (chain a): “The S variant of human ALPHA1-antitrypsin, structure and implications for function and metabolism”. X-ray diffraction, 3 ligands (CYS, NAG, MAN), 3 pockets (best druggability 0.52). MolNFT v1 #191205…
- PDB
- 8API
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1 antitrypsin (chain a); Alpha-1 antitrypsin (chain B)
- UniProt
- P01009
- Ligands
- CYS, NAG, MAN
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1 antitrypsin (chain a) | protein | 340 | 30% helix, 34% strand | P01009 |
| B | Alpha-1 antitrypsin (chain B) | protein | 36 | 0% helix, 50% strand | P01009 |
Ligands and binding sites
- CYS · Cysteine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
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 | 75 | 0.52 | 0.85 | 12 | empty |
| 2 | 54 | 0.39 | 0.81 | 14 | empty |
| 3 | 99 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2521 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan, 1 covalent (N-glycosylation, covalent ligand).
Compared structures
- 8API · The S variant of human ALPHA1-antitrypsin, structure and implications for function and… · the same entry in another collection · chain A against A, TM-score 1.00
- P01009 · AlphaFold monomer V2.0 prediction for alpha-1-antitrypsin (P01009) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 P01009
- Elsewhere: RCSB PDB 8API · PDBe 8API · UniProt P01009
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