Research workbench
Crystal structure of urokinase-type plasminogen activator (upa) complexed with bicyclic peptide UK749
Analyse Crystal structure of urokinase-type plasminogen activator (upa) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MNW
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator chain B; Bicyclic peptide UK749
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- ZBR, SO4, NH2
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator chain B (EC 3.4.21.73) | protein | 245 | 11% helix, 40% strand | P00749 |
| B | Bicyclic peptide UK749 | protein | 13 | 0% helix, 8% strand | — |
Ligands and binding sites
- ZBR · 1,3,5-tris(bromomethyl)benzene · ligand · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- NH2 · Amino group · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A
- 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 | 65 | 0.38 | 0.79 | 16 | empty |
| 2 | 61 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 4MNW · 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 4MNW · PDBe 4MNW · UniProt P00749
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