Research workbench
The crystal structure of a cold-adapted acylaminoacyl peptidase reveals a novel quaternary architecture based on the arm-exchange mechanism
Analyse The crystal structure of a cold-adapted acylaminoacyl peptidase reveals a novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L8S
- Type
- protein
- Length
- 2,416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amino acyl peptidase
- UniProt
- E1VFE0
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Amino acyl peptidase | protein | 604 | 19% helix, 35% strand | E1VFE0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.80 | 0.83 | 80 | empty |
| 2 | 572 | 0.77 | 0.83 | 58 | empty |
| 3 | 577 | 0.77 | 0.83 | 59 | empty |
| 4 | 574 | 0.76 | 0.83 | 55 | empty |
| 5 | 750 | 0.75 | 0.80 | 59 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1936 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1896 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 321 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5L8S · The crystal structure of a cold-adapted acylaminoacyl peptidase reveals a novel… · 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
- Every structure of UniProt E1VFE0
- Elsewhere: RCSB PDB 5L8S · PDBe 5L8S · UniProt E1VFE0
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