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Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)
Analyse Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWP
- Type
- protein
- Length
- 604 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.28
- Source
- Homo sapiens; Vicugna pacos
- Molecule
- Plasminogen Activator Inhibitor-1; VHH-2g-42; VHH-2w-64
- UniProt
- P05121
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · resolution 2.28 · 3 distinct chains · 20% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen Activator Inhibitor-1 | protein | 368 | 29% helix, 31% strand | P05121 |
| B | VHH-2g-42 | protein | 115 | 8% helix, 54% strand | — |
| C | VHH-2w-64 | protein | 121 | 2% helix, 49% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.57 | 0.81 | 20 | empty |
| 2 | 106 | 0.42 | 0.77 | 19 | empty |
| 3 | 53 | 0.42 | 0.83 | 20 | empty |
| 4 | 52 | 0.42 | 0.82 | 15 | empty |
| 5 | 132 | 0.39 | 0.74 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–C · 807 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 672 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6GWP · Crystal structure of stabilized active plasminogen activator inhibitor-1 (pai-1-stab) in… · 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 0.97
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
- Elsewhere: RCSB PDB 6GWP · PDBe 6GWP · UniProt P05121
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