MolNFT v1 · #140649 · protein
Proline iminopeptidase from psychrophilic yeast glaciozyma antarctica
5YHP · Cold active proline iminopeptidase: “Proline iminopeptidase from psychrophilic yeast glaciozyma antarctica”. X-ray diffraction, 8 pockets (best druggability 0.69). MolNFT v1 #140649 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YHP
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cold active proline iminopeptidase
- EC
- 3.4.11.5
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cold active proline iminopeptidase (EC 3.4.11.5) | protein | 318 | 44% helix, 16% strand | — |
| B | Cold active proline iminopeptidase (EC 3.4.11.5) | protein | 319 | 45% helix, 16% strand | — |
Ligands and binding sites
- FLC · Citrate anion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.69 | 0.85 | 32 | FLC |
| 2 | 277 | 0.68 | 0.84 | 37 | FLC |
| 3 | 77 | 0.33 | 0.74 | 16 | empty |
| 4 | 74 | 0.32 | 0.74 | 14 | empty |
| 5 | 65 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1251 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5YHP · Proline iminopeptidase from Psychrophilic yeast glaciozyma antarctica · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5YHP · PDBe 5YHP
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