MolNFT v1 · #59268 · protein
Structure of urokinase receptor, urokinase and vitronectin complex
3BT1 · Urokinase-type plasminogen activator: “Structure of urokinase receptor, urokinase and vitronectin complex”. X-ray diffraction, 2 ligands (NAG, MAN), 7 pockets (best druggability 0.58). MolNFT v1 #59268 on GenesisL1: 3D structure…
- PDB
- 3BT1
- Type
- protein
- Length
- 438 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Vitronectin; Urokinase plasminogen activator…
- UniProt
- P00749, P04004, Q03405
- Ligands
- NAG, MAN
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator | protein | 125 | 6% helix, 23% strand | P00749 |
| B | Vitronectin | protein | 40 | 20% helix, 5% strand | P04004 |
| U | Urokinase plasminogen activator surface receptor | protein | 273 | 4% helix, 47% strand | Q03405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains U
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.58 | 0.88 | 26 | empty |
| 2 | 268 | 0.57 | 0.78 | 39 | empty |
| 3 | 304 | 0.55 | 0.76 | 47 | empty |
| 4 | 167 | 0.53 | 0.79 | 29 | empty |
| 5 | 60 | 0.42 | 0.82 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–U · 1364 Ų buried · 16 hydrogen bonds · protein-protein
- B–U · 660 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3BT1 · Structure of urokinase receptor, urokinase and vitronectin complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q03405 · AlphaFold monomer V2.0 prediction for urokinase plasminogen activator surface receptor… · a predicted model of the same protein · chain U against A, TM-score 0.97
- P04004 · AlphaFold monomer V2.0 prediction for vitronectin (P04004) · a predicted model of the same protein · chain B against A, TM-score 0.79
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
- Every structure of UniProt P04004
- Every structure of UniProt Q03405
- Elsewhere: RCSB PDB 3BT1 · PDBe 3BT1 · UniProt P00749 · UniProt P04004 · UniProt Q03405
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