Research workbench
Cryoem structure of human presequence protease in partial closed state 1
Analyse Cryoem structure of human presequence protease in partial closed state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XOV
- Type
- protein
- Length
- 972 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Presequence protease, mitochondrial; Amyloid-beta precursor protein
- EC
- 3.4.24.-
- UniProt
- Q5JRX3, P05067
- Pockets
- 10 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Presequence protease, mitochondrial (EC 3.4.24.-) | protein | 966 | 45% helix, 15% strand | Q5JRX3 |
| B | Amyloid-beta precursor protein | protein | 3 | 0% helix, 0% strand | P05067 |
| C | Amyloid-beta precursor protein | protein | 3 | 0% helix, 0% strand | — |
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.73 | 0.77 | 82 | empty |
| 2 | 457 | 0.70 | 0.81 | 33 | empty |
| 3 | 657 | 0.69 | 0.77 | 73 | empty |
| 4 | 180 | 0.68 | 0.87 | 35 | empty |
| 5 | 283 | 0.65 | 0.82 | 36 | empty |
Interfaces
2 interfaces between chains.
- A–B · 364 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 238 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XOV · CryoEM structure of human presequence protease in partial closed state 1 · the same entry in another collection · 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 B against A, TM-score 1.00
- Q5JRX3 · AlphaFold monomer V2.0 prediction for presequence protease, mitochondrial (Q5JRX3) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5JRX3
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 6XOV · PDBe 6XOV · UniProt Q5JRX3 · UniProt P05067
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