Research workbench
X-ray crystal structure of the complex of microplasminogen with alpha domain of streptokinase in the presence cadmium ions
Analyse X-ray crystal structure of the complex of microplasminogen with alpha domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L4Z
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasminogen; Streptokinase
- EC
- 3.4.21.7
- UniProt
- P00747, P00779
- Ligands
- CD
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasminogen (EC 3.4.21.7) | protein | 248 | 10% helix, 34% strand | P00747 |
| B | Streptokinase | protein | 125 | 13% helix, 38% strand | P00779 |
Ligands and binding sites
- CD · Cadmium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.48 | 0.79 | 24 | empty |
| 2 | 51 | 0.42 | 0.83 | 13 | empty |
| 3 | 56 | 0.35 | 0.79 | 16 | empty |
| 4 | 50 | 0.34 | 0.79 | 18 | empty |
| 5 | 55 | 0.27 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1L4Z · X-ray crystal structure of the complex of microplasminogen with alpha domain of… · 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 0.95
- P00779 · AlphaFold monomer V2.0 prediction for streptokinase C (P00779) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 1L4Z · PDBe 1L4Z · UniProt P00747 · UniProt P00779
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