Research workbench
Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding
Analyse Crystal structure of aprotinin in complex with sucrose octasulfate: unusual… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LDJ
- Type
- protein
- Length
- 168 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic trypsin inhibitor
- UniProt
- P00974
- Ligands
- GU4, YYJ
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pancreatic trypsin inhibitor | protein | 56 | 21% helix, 27% strand | P00974 |
Ligands and binding sites
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains B, C
- YYJ · 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose · ligand · chains B, C
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.43 | 0.76 | 30 | empty |
| 2 | 144 | 0.42 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 355 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 318 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 3LDJ · Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions… · the same entry in another collection · chain A against A, TM-score 1.00
- P00974 · AlphaFold monomer V2.0 prediction for pancreatic trypsin inhibitor (P00974) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P00974
- Elsewhere: RCSB PDB 3LDJ · PDBe 3LDJ · UniProt P00974
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.