MolNFT v1 · #102646 · protein
Crystal structure of urokinase-type plasminogen activator (upa) complexed with bicyclic peptide UK601 (bicyclic 1)
4OS1: “Crystal structure of urokinase-type plasminogen activator (upa) complexed with bicyclic peptide UK601…”. X-ray diffraction, 2 ligands (SO4, NH2), 2 pockets (best druggability 0.37). MolNFT v1 #102646 on GenesisL1: 3D structure…
- PDB
- 4OS1
- Type
- protein
- Length
- 259 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Bicyclic peptide UK601 (bicyclic 1)
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- SO4, NH2
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 245 | 11% helix, 39% strand | P00749 |
| B | Bicyclic peptide UK601 (bicyclic 1) | protein | 14 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- NH2 · Amino group · ion · chains B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.37 | 0.77 | 16 | empty |
| 2 | 74 | 0.31 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 733 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4OS1 · Crystal structure of urokinase-type plasminogen activator (uPA) complexed with bicyclic… · 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 4OS1 · PDBe 4OS1 · UniProt P00749
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