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
- 3LDM
- Type
- protein
- Length
- 280 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pancreatic trypsin inhibitor
- UniProt
- P00974
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Pancreatic trypsin inhibitor | protein | 56 | 21% helix, 27% strand | P00974 |
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 | 587 | 0.65 | 0.76 | 39 | empty |
| 2 | 112 | 0.36 | 0.73 | 19 | empty |
| 3 | 114 | 0.34 | 0.72 | 20 | empty |
| 4 | 96 | 0.33 | 0.73 | 16 | empty |
| 5 | 84 | 0.33 | 0.74 | 14 | empty |
Interfaces
5 interfaces between chains.
- C–D · 382 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 336 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 321 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 318 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 3LDM · 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 B 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 3LDM · PDBe 3LDM · UniProt P00974
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