Research workbench
Crystal structure of the catalytic domain of a multi-domain alginate lyase DP0100 from thermophilic bacterium defluviitalea phaphyphila
Analyse Crystal structure of the catalytic domain of a multi-domain alginate lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JP4
- Type
- protein
- Length
- 3,080 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase
- Ligands
- CA, MN, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Alginate lyase | protein | 770 | 29% helix, 28% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- CAC · Cacodylate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.74 | 0.78 | 103 | empty |
| 2 | 550 | 0.69 | 0.80 | 74 | empty |
| 3 | 223 | 0.66 | 0.85 | 61 | empty |
| 4 | 168 | 0.63 | 0.86 | 43 | empty |
| 5 | 317 | 0.63 | 0.80 | 49 | empty |
Interfaces
3 interfaces between chains.
- A–C · 416 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 176 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 126 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6JP4 · Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from… · 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 6JP4 · PDBe 6JP4
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