MolNFT v1 · #51994 · protein
Urokinase-type plasminogen activator inhibitor complex with a 1-(7-SULPHOAMIDOISOQUINOLINYL)GUANIDINE
2VNT: “Urokinase-type plasminogen activator inhibitor complex with a 1-(7-SULPHOAMIDOISOQUINOLINYL)GUANIDINE”. X-ray diffraction, 2 ligands (QGG, SO4), 10 pockets (best druggability 0.86). MolNFT v1 #51994 on GenesisL1: 3D structure…
- PDB
- 2VNT
- Type
- protein
- Length
- 1,545 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urokinase-type plasminogen activator
- EC
- 3.4.21.73
- UniProt
- P00749
- Ligands
- QGG, SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 257 | 11% helix, 37% strand | P00749 |
| B, D, E | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 258 | 11% helix, 38% strand | P00749 |
| C | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 258 | 10% helix, 34% strand | P00749 |
| F | Urokinase-type plasminogen activator (EC 3.4.21.73) | protein | 256 | 11% helix, 35% strand | P00749 |
Ligands and binding sites
- QGG · 1-({4-chloro-1-[(diaminomethylidene)amino]isoquinolin-7-yl}sulfonyl)-D-proline · ligand · 6 copies · chains A, D, B, F, C, E
- SO4 · Sulfate ion · ion · 9 copies · chains B, C, E, D, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.86 | 0.87 | 134 | SO4, QGG |
| 2 | 480 | 0.80 | 0.87 | 71 | SO4 |
| 3 | 546 | 0.80 | 0.86 | 81 | QGG |
| 4 | 531 | 0.79 | 0.86 | 77 | QGG |
| 5 | 265 | 0.74 | 0.88 | 34 | empty |
Interfaces
9 interfaces between chains.
- B–C · 657 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 637 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 630 Ų buried · 3 hydrogen bonds · protein-protein
- B–E · 628 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 2VNT · Urokinase-Type Plasminogen Activator Inhibitor Complex with a 1-(7… · 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 2VNT · PDBe 2VNT · UniProt P00749
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