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Crystal structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1
Analyse Crystal structure of a novel small molecule inactivator bound to plasminogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G8R
- Type
- protein
- Length
- 725 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor-1
- UniProt
- P05121
- Ligands
- 96P, SO4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen activator inhibitor-1 | protein | 357 | 31% helix, 32% strand | P05121 |
| B | Plasminogen activator inhibitor-1 | protein | 368 | 31% helix, 32% strand | P05121 |
Ligands and binding sites
- 96P · (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate) · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.73 | 0.78 | 77 | empty |
| 2 | 132 | 0.58 | 0.84 | 24 | empty |
| 3 | 150 | 0.57 | 0.82 | 25 | empty |
| 4 | 169 | 0.52 | 0.79 | 31 | empty |
| 5 | 61 | 0.48 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 829 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4G8R · Crystal Structure of a novel small molecule inactivator bound to plasminogen activator… · the same entry in another collection · chain A against A, TM-score 1.00
- P05121 · AlphaFold monomer V2.0 prediction for plasminogen activator inhibitor 1 (P05121) · a predicted model of the same protein · chain A against A, TM-score 0.99
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
- Elsewhere: RCSB PDB 4G8R · PDBe 4G8R · UniProt P05121
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