Research workbench
The crystal structure of the double-headed arrowhead protease inhibitor a in complex with two trypsins
Analyse The crystal structure of the double-headed arrowhead protease inhibitor a in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E8L
- Type
- protein
- Length
- 622 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine proteinase inhibitor a; Cationic trypsin
- EC
- 3.4.21.4
- UniProt
- Q7M1P4, P00760
- Ligands
- CA, NA, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Serine proteinase inhibitor a | protein | 176 | 2% helix, 47% strand | Q7M1P4 |
| A, B | Cationic trypsin (EC 3.4.21.4) | protein | 223 | 10% helix, 35% strand | P00760 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, C, B
- NA · Sodium ion · metal · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains C, B, A
- GOL · Glycerol · additive · 7 copies · chains C, A, B
- ACT · Acetate ion · additive · 4 copies · chains C, A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.78 | 0.95 | 34 | EDO |
| 2 | 257 | 0.59 | 0.79 | 30 | GOL, ACT |
| 3 | 55 | 0.56 | 0.90 | 19 | empty |
| 4 | 113 | 0.42 | 0.76 | 20 | GOL |
| 5 | 126 | 0.41 | 0.75 | 20 | GOL |
Interfaces
2 interfaces between chains.
- C–B · 1078 Ų buried · 17 hydrogen bonds · protein-protein
- C–A · 826 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 3E8L · The Crystal Structure of the Double-headed Arrowhead Protease Inhibitor A in Complex with… · the same entry in another collection · chain C against C, TM-score 1.00
- 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain A against A, TM-score 1.00
- 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · 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 Q7M1P4
- Every structure of UniProt P00760
- Elsewhere: RCSB PDB 3E8L · PDBe 3E8L · UniProt Q7M1P4 · UniProt P00760
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