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
- 3LDI
- Type
- protein
- Length
- 286 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic trypsin inhibitor
- UniProt
- P00974
- Ligands
- HG, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Pancreatic trypsin inhibitor | protein | 57 | 21% helix, 26% strand | P00974 |
| B, D | Pancreatic trypsin inhibitor | protein | 58 | 21% helix, 26% strand | P00974 |
| C | Pancreatic trypsin inhibitor | protein | 56 | 21% helix, 27% strand | P00974 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.67 | 0.74 | 40 | SO4 |
| 2 | 131 | 0.39 | 0.74 | 20 | HG |
| 3 | 137 | 0.38 | 0.73 | 19 | HG |
| 4 | 108 | 0.36 | 0.73 | 19 | HG |
| 5 | 103 | 0.35 | 0.73 | 17 | HG |
Interfaces
5 interfaces between chains.
- A–B · 322 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 4 hydrogen bonds · protein-protein
- D–E · 310 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 308 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 298 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 3LDI · Crystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions… · the same entry in another collection · chain E against E, 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 0.98
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 P00974
- Elsewhere: RCSB PDB 3LDI · PDBe 3LDI · UniProt P00974
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.