Research workbench
Human mesotrypsin complexed with amyloid precursor protein INHIBITOR(APPI)
Analyse Human mesotrypsin complexed with amyloid precursor protein INHIBITOR(APPI) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L33
- Type
- protein
- Length
- 1,104 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trypsin-3; Amyloid beta A4 protein
- EC
- 3.4.21.4
- UniProt
- P35030, P05067
- Ligands
- CA
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Trypsin-3 (EC 3.4.21.4) | protein | 224 | 11% helix, 35% strand | P35030 |
| E, F, G, H | Amyloid beta A4 protein | protein | 52 | 13% helix, 31% strand | P05067 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 19 copies · chains A, C, E, B, F, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.64 | 0.76 | 48 | FMT |
| 2 | 271 | 0.53 | 0.76 | 40 | FMT |
| 3 | 109 | 0.49 | 0.81 | 22 | empty |
| 4 | 115 | 0.48 | 0.80 | 23 | empty |
| 5 | 188 | 0.46 | 0.75 | 34 | FMT |
Interfaces
8 interfaces between chains.
- A–C · 810 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 627 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 622 Ų buried · 14 hydrogen bonds · protein-protein
- D–H · 622 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 590 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 3L33 · Human mesotrypsin complexed with amyloid precursor protein inhibitor(APPI) · the same entry in another collection · chain H against H, TM-score 1.00
- P35030 · AlphaFold monomer V2.0 prediction for trypsin-3 (P35030) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain G 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 P35030
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 3L33 · PDBe 3L33 · UniProt P35030 · UniProt P05067
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