Research workbench
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
- 4G8O
- Type
- protein
- Length
- 1,452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor 1
- UniProt
- P05121
- Ligands
- 96P, SO4
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasminogen activator inhibitor 1 | protein | 359 | 31% helix, 32% strand | P05121 |
| C, D | Plasminogen activator inhibitor 1 | protein | 367 | 29% helix, 31% strand | P05121 |
Ligands and binding sites
- 96P · (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate) · ligand · chains D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 643 | 0.71 | 0.78 | 58 | empty |
| 2 | 569 | 0.69 | 0.78 | 63 | empty |
| 3 | 747 | 0.68 | 0.76 | 72 | SO4 |
| 4 | 155 | 0.58 | 0.82 | 24 | empty |
| 5 | 193 | 0.56 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 885 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 708 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4G8O · 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 0.98
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 4G8O · PDBe 4G8O · UniProt P05121
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