Research workbench
Human mesotrypsin in complex with amyloid precursor protein inhibitor variant appi-M17G/I18F/F34V
Analyse Human mesotrypsin in complex with amyloid precursor protein inhibitor variant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C67
- Type
- protein
- Length
- 555 residues
- Chains
- 4
- 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
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trypsin-3 (EC 3.4.21.4) | protein | 224 | 11% helix, 35% strand | P35030 |
| E | Amyloid beta A4 protein | protein | 54 | 20% helix, 30% strand | P05067 |
| C | Amyloid beta A4 protein | protein | 53 | 13% helix, 30% strand | P05067 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.51 | 0.76 | 27 | empty |
| 2 | 154 | 0.42 | 0.74 | 34 | empty |
| 3 | 110 | 0.38 | 0.75 | 19 | empty |
| 4 | 59 | 0.29 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 674 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 615 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5C67 · Human Mesotrypsin in complex with amyloid precursor protein inhibitor variant… · the same entry in another collection · chain A against A, 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 0.99
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 5C67 · PDBe 5C67 · UniProt P35030 · UniProt P05067
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