Research workbench
Structural and functional characterization of a novel archaeal phosphodiesterase
Analyse Structural and functional characterization of a novel archaeal phosphodiesterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S3L
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein MJ0936
- UniProt
- Q58346
- Ligands
- UNX, PO4
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein MJ0936 | protein | 165 | 25% helix, 35% strand | Q58346 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.35 | 0.77 | 16 | empty |
| 2 | 57 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 454 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1S3L · Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase · the same entry in another collection · chain A against A, TM-score 1.00
- Q58346 · AlphaFold monomer V2.0 prediction for phosphodiesterase MJ0936 (Q58346) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q58346
- Elsewhere: RCSB PDB 1S3L · PDBe 1S3L · UniProt Q58346
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