Research workbench
A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site
Analyse A novel serine protease inhibition motif involving a multi-centered short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GI8
- Type
- protein
- Length
- 254 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- BMZ
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator | protein | 9 | 0% helix, 0% strand | P00749 |
| B | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 245 | 11% helix, 39% strand | P00749 |
Ligands and binding sites
- BMZ · 2-(2-hydroxy-phenyl)-1H-benzoimidazole-5-carboxamidine · ligand · chains B
- CIT · Citric acid · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.41 | 0.75 | 30 | BMZ |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1GI8 · A novel serine protease inhibition motif involving a multi-centered short hydrogen… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00749
- Elsewhere: RCSB PDB 1GI8 · PDBe 1GI8 · UniProt P00749
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