Research workbench
Crystal structure of zebrafish plasminogen activator inhibitor-1 (pai- 1)
Analyse Crystal structure of zebrafish plasminogen activator inhibitor-1 (pai- 1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DTE
- Type
- protein
- Length
- 738 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1)…
- UniProt
- F1QRB8
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 | protein | 374 | 30% helix, 30% strand | F1QRB8 |
| B | Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 | protein | 364 | 31% helix, 32% strand | F1QRB8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.45 | 0.77 | 19 | empty |
| 2 | 86 | 0.42 | 0.79 | 19 | empty |
| 3 | 55 | 0.41 | 0.82 | 15 | empty |
| 4 | 64 | 0.38 | 0.79 | 18 | empty |
| 5 | 102 | 0.37 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 456 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 4DTE · Crystal structure of zebrafish plasminogen activator inhibitor-1 (PAI-1) · the same entry in another collection · chain B against B, 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 F1QRB8
- Elsewhere: RCSB PDB 4DTE · PDBe 4DTE · UniProt F1QRB8
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