MolNFT v1 · #145982 · protein
Highly potent and selective plasmin inhibitors based on the sunflower trypsin inhibitor-1 scaffold attenuate fibrinolysis in plasma
6D3X · Plasminogen: “Highly potent and selective plasmin inhibitors based on the sunflower trypsin inhibitor-1 scaffold attenuate…”. X-ray diffraction, 4 pockets (best druggability 0.83). MolNFT v1 #145982 on GenesisL1: 3D structure…
- PDB
- 6D3X
- Type
- protein
- Length
- 516 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen; Trypsin inhibitor 1
- EC
- 3.4.21.7
- UniProt
- P00747, Q4GWU5
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasminogen (EC 3.4.21.7) | protein | 244 | 10% helix, 36% strand | P00747 |
| C, D | Trypsin inhibitor 1 | protein | 14 | 0% helix, 36% strand | Q4GWU5 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.83 | 0.93 | 39 | empty |
| 2 | 181 | 0.47 | 0.75 | 35 | empty |
| 3 | 81 | 0.36 | 0.76 | 16 | empty |
| 4 | 75 | 0.34 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–D · 644 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 327 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 273 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6D3X · Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1… · the same entry in another collection · chain A against A, TM-score 1.00
- P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q4GWU5 · AlphaFold monomer V2.0 prediction for trypsin inhibitor 1 (Q4GWU5) · a predicted model of the same protein · chain C against A, TM-score 0.40
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 P00747
- Every structure of UniProt Q4GWU5
- Elsewhere: RCSB PDB 6D3X · PDBe 6D3X · UniProt P00747 · UniProt Q4GWU5
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