Research workbench
The crystal structure of upain-1-W3A in complex with upa at PH7.4
Analyse The crystal structure of upain-1-W3A in complex with upa at PH7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZKO
- Type
- protein
- Length
- 251 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; N-terminal fragment of upain-1-W3A; C-terminal…
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 247 | 11% helix, 39% strand | P00749 |
| P | N-terminal fragment of upain-1-W3A | protein | 2 | 0% helix, 0% strand | — |
| Q | C-terminal fragment of upain-1-W3A | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 136 | 0.42 | 0.75 | 22 | SO4 |
Interfaces
3 interfaces between chains.
- U–P · 248 Ų buried · 11 hydrogen bonds · protein-protein
- U–Q · 141 Ų buried · 5 hydrogen bonds · protein-protein
- P–Q · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4ZKO · The crystal structure of upain-1-W3A in complex with uPA at pH7.4 · the same entry in another collection · chain U against U, 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 4ZKO · PDBe 4ZKO · UniProt P00749
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