Research workbench
Combinatorial engineering of proteolytically resistant appi variants that selectively inhibit human kallikrein 6 for cancer therapy
Analyse Combinatorial engineering of proteolytically resistant appi variants that… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NX3
- Type
- protein
- Length
- 330 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kallikrein-6; Amyloid-beta A4 protein
- EC
- 3.4.21.-
- UniProt
- Q92876, P05067
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kallikrein-6 (EC 3.4.21.-) | protein | 222 | 10% helix, 37% strand | Q92876 |
| B | Amyloid-beta A4 protein | protein | 13 | 23% helix, 0% strand | P05067 |
| D | Amyloid-beta A4 protein | protein | 42 | 19% helix, 36% strand | P05067 |
| C | Amyloid-beta A4 protein | protein | 53 | 13% helix, 30% strand | P05067 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.55 | 0.77 | 46 | empty |
| 2 | 74 | 0.35 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 726 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 618 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 453 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 69 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5NX3 · Combinatorial Engineering of Proteolytically Resistant APPI Variants that Selectively… · the same entry in another collection · chain C against C, TM-score 1.00
- Q92876 · AlphaFold monomer V2.0 prediction for kallikrein-6 (Q92876) · 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 C against A, TM-score 0.96
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 Q92876
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 5NX3 · PDBe 5NX3 · UniProt Q92876 · UniProt P05067
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