Research workbench
Prolyl oligopeptidase B from galerina marginata bound to 25MER macrocyclization substrate - D661A 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
- 5N4D
- 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
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl oligopeptidase | protein | 720 | 22% helix, 33% strand | H2E7Q8 |
| B | Prolyl oligopeptidase | protein | 722 | 22% helix, 33% strand | H2E7Q8 |
| C, D | Alpha-amanitin proprotein | protein | 18 | 0% helix, 0% strand | H2E7Q5 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.83 | 0.84 | 107 | empty |
| 2 | 743 | 0.81 | 0.84 | 88 | GOL |
| 3 | 478 | 0.80 | 0.87 | 65 | empty |
| 4 | 1020 | 0.77 | 0.79 | 73 | empty |
| 5 | 378 | 0.74 | 0.85 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1238 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1236 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5N4D · 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 B 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 5N4D · PDBe 5N4D · UniProt H2E7Q8 · UniProt H2E7Q5
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