Research workbench
The ligand free catalytic domain of murine urokinase-type plasminogen activator
Analyse The ligand free catalytic domain of murine urokinase-type plasminogen activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LHS
- Type
- protein
- Length
- 896 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P06869
- Ligands
- NI, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 224 | 9% helix, 41% strand | P06869 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 4 copies · chains B, A, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains B, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 682 | 0.86 | 0.90 | 61 | empty |
| 2 | 655 | 0.85 | 0.90 | 58 | NI |
| 3 | 55 | 0.63 | 0.94 | 22 | empty |
| 4 | 51 | 0.59 | 0.92 | 23 | empty |
| 5 | 65 | 0.58 | 0.90 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1054 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1048 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1015 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 998 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 351 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5LHS · The ligand free catalytic domain of murine urokinase-type plasminogen activator · the same entry in another collection · chain B against B, TM-score 1.00
- P06869 · AlphaFold monomer V2.0 prediction for urokinase-type plasminogen activator (P06869) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 P06869
- Elsewhere: RCSB PDB 5LHS · PDBe 5LHS · UniProt P06869
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