MolNFT v1 · #100118 · protein
Crystal structure of urokinase-type plasminogen activator (upa) complexed with bicyclic peptide UK903
4MNY · Urokinase-type plasminogen activator chain B: “Crystal structure of urokinase-type plasminogen activator (upa) complexed with bicyclic peptide UK903”. X-ray diffraction, 3 ligands (29O, SO4, NH2), 5 pockets (best druggability 0.62).…
- PDB
- 4MNY
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator chain B; Bicyclic peptide UK903
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- 29O, SO4, NH2
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Urokinase-type plasminogen activator chain B (EC 3.4.21.73) | protein | 245 | 11% helix, 39% strand | P00749 |
| C, D | Bicyclic peptide UK903 | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- 29O · N,N',N''-benzene-1,3,5-triyltris(2-bromoacetamide) · ligand · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 5 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.62 | 0.78 | 37 | SO4, ACT, 29O |
| 2 | 283 | 0.59 | 0.78 | 36 | ACT, 29O |
| 3 | 239 | 0.49 | 0.75 | 33 | empty |
| 4 | 67 | 0.48 | 0.84 | 25 | empty |
| 5 | 158 | 0.41 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 604 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 592 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 covalent (disulfide, covalent ligand).
Compared structures
- 4MNY · 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 4MNY · PDBe 4MNY · UniProt P00749
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