Research workbench
Complex of the catalytic domain of human plasmin and streptokinase
Analyse Complex of the catalytic domain of human plasmin and streptokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BML
- Type
- protein
- Length
- 1,136 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmin; Streptokinase
- EC
- 3.4.21.7
- UniProt
- P00747, P00779
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmin (EC 3.4.21.7) | protein | 250 | 8% helix, 33% strand | P00747 |
| C, D | Streptokinase | protein | 318 | 11% helix, 42% strand | P00779 |
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.74 | 0.79 | 84 | empty |
| 2 | 580 | 0.73 | 0.80 | 68 | empty |
| 3 | 379 | 0.62 | 0.78 | 39 | empty |
| 4 | 366 | 0.60 | 0.77 | 38 | empty |
| 5 | 125 | 0.58 | 0.85 | 36 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2179 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 2120 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 975 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 197 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 1BML · Complex of the catalytic domain of human plasmin and streptokinase · the same entry in another collection · chain A against A, TM-score 1.00
- P00779 · AlphaFold monomer V2.0 prediction for streptokinase C (P00779) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P00747 · AlphaFold monomer V2.0 prediction for plasminogen (P00747) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00779
- Elsewhere: RCSB PDB 1BML · PDBe 1BML · UniProt P00747 · UniProt P00779
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