Research workbench
Crystal structure of the plasmin-textilinin-1 complex
Analyse Crystal structure of the plasmin-textilinin-1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UIR
- Type
- protein
- Length
- 601 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmin light chain B; Textilinin-1
- EC
- 3.4.21.7
- UniProt
- P00747, Q90WA1
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasmin light chain B (EC 3.4.21.7) | protein | 243 | 10% helix, 33% strand | P00747 |
| B | Plasmin light chain B (EC 3.4.21.7) | protein | 245 | 10% helix, 33% strand | P00747 |
| C | Textilinin-1 | protein | 56 | 27% helix, 29% strand | Q90WA1 |
| D | Textilinin-1 | protein | 57 | 19% helix, 28% strand | Q90WA1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
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 | 169 | 0.46 | 0.76 | 27 | empty |
| 2 | 165 | 0.44 | 0.74 | 24 | empty |
| 3 | 71 | 0.32 | 0.75 | 14 | empty |
| 4 | 67 | 0.31 | 0.75 | 16 | empty |
| 5 | 62 | 0.26 | 0.72 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 709 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 697 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3UIR · Crystal structure of the plasmin-textilinin-1 complex · the same entry in another collection · chain D against D, 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 0.98
- Q90WA1 · AlphaFold monomer V2.0 prediction for kunitz-type serine protease inhibitor textilinin-1… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q90WA1
- Elsewhere: RCSB PDB 3UIR · PDBe 3UIR · UniProt P00747 · UniProt Q90WA1
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