Research workbench
Crystal structure of a lyase from Alteromonas sp.
Analyse Crystal structure of a lyase from Alteromonas sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JQ9
- Type
- protein
- Length
- 965 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.81
- Source
- Alteromonas sp. LOR
- Molecule
- Short ulvan lyase
- UniProt
- A0A109PTH9
- Ligands
- CA, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.81 · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short ulvan lyase | protein | 482 | 6% helix, 43% strand | A0A109PTH9 |
| B | Short ulvan lyase | protein | 483 | 6% helix, 44% strand | A0A109PTH9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 994 | 0.76 | 0.79 | 79 | empty |
| 2 | 1077 | 0.75 | 0.78 | 85 | empty |
| 3 | 465 | 0.58 | 0.73 | 38 | empty |
| 4 | 94 | 0.36 | 0.75 | 21 | SO4 |
| 5 | 55 | 0.31 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 542 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6JQ9 · Crystal structure of a lyase from alteromonas sp. · 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 A0A109PTH9
- Elsewhere: RCSB PDB 6JQ9 · PDBe 6JQ9 · UniProt A0A109PTH9
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