Research workbench
Crystal structure of stabilized active plasminogen activator inhibitor-1 (pai-1-W175F) in complex with an inhibitory nanobody (vhh-S-A93, NB93)
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
- 6ZRV
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen activator inhibitor 1; Vhh-S-A93 (NB93)
- UniProt
- P05121
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen activator inhibitor 1 | protein | 371 | 29% helix, 31% strand | P05121 |
| B | Vhh-S-A93 (NB93) | protein | 123 | 2% helix, 48% strand | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.49 | 0.84 | 19 | empty |
| 2 | 54 | 0.42 | 0.83 | 15 | empty |
| 3 | 67 | 0.42 | 0.81 | 23 | empty |
| 4 | 63 | 0.37 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1013 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ZRV · Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) 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 0.96
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 6ZRV · PDBe 6ZRV · UniProt P05121
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