Research workbench
Prolyl oligopeptidase B from galerina marginata bound to 25MER macrocyclization substrate - S577A mutant
Analyse Prolyl oligopeptidase B from galerina marginata bound to 25MER macrocyclization… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N4B
- Type
- protein
- Length
- 1,478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl oligopeptidase; Alpha-amanitin proprotein
- UniProt
- H2E7Q8, H2E7Q5
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prolyl oligopeptidase | protein | 722 | 22% helix, 33% strand | H2E7Q8 |
| D, C | Alpha-amanitin proprotein | protein | 17 | 0% helix, 0% strand | H2E7Q5 |
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 652 | 0.79 | 0.84 | 91 | empty |
| 2 | 221 | 0.77 | 0.91 | 51 | empty |
| 3 | 182 | 0.77 | 0.93 | 38 | empty |
| 4 | 297 | 0.74 | 0.87 | 42 | empty |
| 5 | 179 | 0.72 | 0.89 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1169 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1167 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1038 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5N4B · Prolyl oligopeptidase B from Galerina marginata bound to 25mer macrocyclization substrate… · the same entry in another collection · chain A against A, TM-score 1.00
- H2E7Q8 · AlphaFold monomer V2.0 prediction for dual function macrocyclase- peptidase popb (H2E7Q8) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 H2E7Q8
- Every structure of UniProt H2E7Q5
- Elsewhere: RCSB PDB 5N4B · PDBe 5N4B · UniProt H2E7Q8 · UniProt H2E7Q5
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