Research workbench
Crystal structure of a michaelis complex between plasminogen activator inhibitor-1 and urokinase-type plasminogen activator
Analyse Crystal structure of a michaelis complex between plasminogen activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PB1
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor 1; Plasminogen activator, urokinase
- EC
- 3.4.21.73
- UniProt
- P05121, Q5SWW8
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Plasminogen activator inhibitor 1 | protein | 375 | 30% helix, 31% strand | P05121 |
| E | Plasminogen activator, urokinase (EC 3.4.21.73) | protein | 247 | 11% helix, 40% strand | Q5SWW8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.66 | 0.79 | 58 | empty |
| 2 | 277 | 0.62 | 0.80 | 42 | empty |
| 3 | 162 | 0.60 | 0.83 | 26 | empty |
| 4 | 65 | 0.40 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- I–E · 1132 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3PB1 · Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and… · the same entry in another collection · chain I against I, TM-score 1.00
- P05121 · AlphaFold monomer V2.0 prediction for plasminogen activator inhibitor 1 (P05121) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 P05121
- Every structure of UniProt Q5SWW8
- Elsewhere: RCSB PDB 3PB1 · PDBe 3PB1 · UniProt P05121 · UniProt Q5SWW8
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