MolNFT v1 · #59269 · protein
Structure of urokinase receptor, urokinase and vitronectin complex
3BT2 · Urokinase-type plasminogen activator: “Structure of urokinase receptor, urokinase and vitronectin complex”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.59). MolNFT v1 #59269 on GenesisL1: 3D structure, binding…
- PDB
- 3BT2
- Type
- protein
- Length
- 846 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator; Vitronectin; Anti-upar antibody, light chain…
- UniProt
- P00749, P04004, Q03405
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator | protein | 124 | 8% helix, 27% strand | P00749 |
| B | Vitronectin | protein | 40 | 10% helix, 5% strand | P04004 |
| L | Anti-upar antibody, light chain | protein | 211 | 6% helix, 51% strand | — |
| H | Anti-upar antibody, heavy chain | protein | 212 | 8% helix, 50% strand | — |
| U | Urokinase plasminogen activator surface receptor | protein | 259 | 5% helix, 51% strand | Q03405 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains U
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.59 | 0.79 | 36 | empty |
| 2 | 358 | 0.58 | 0.76 | 35 | empty |
| 3 | 280 | 0.53 | 0.75 | 44 | empty |
| 4 | 138 | 0.48 | 0.79 | 25 | empty |
| 5 | 163 | 0.44 | 0.76 | 18 | empty |
Interfaces
5 interfaces between chains.
- L–H · 1737 Ų buried · 18 hydrogen bonds · protein-protein
- A–U · 1267 Ų buried · 12 hydrogen bonds · protein-protein
- B–U · 622 Ų buried · 10 hydrogen bonds · protein-protein
- H–U · 450 Ų buried · 11 hydrogen bonds · protein-protein
- L–U · 260 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3BT2 · Structure of urokinase receptor, urokinase and vitronectin complex · the same entry in another collection · chain B against B, 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 0.98
- P04004 · AlphaFold monomer V2.0 prediction for vitronectin (P04004) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 3BT2 · PDBe 3BT2 · UniProt P00749 · UniProt P04004 · UniProt Q03405
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