Research workbench
PL6 alginate lyase BCALYPL6
Analyse PL6 alginate lyase BCALYPL6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DMK
- Type
- protein
- Length
- 2,924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BCALYPL6
- UniProt
- A0A1Y4JW59
- Ligands
- CA
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BCALYPL6 | protein | 732 | 5% helix, 43% strand | A0A1Y4JW59 |
| B | BCALYPL6 | protein | 732 | 5% helix, 42% strand | A0A1Y4JW59 |
| C | BCALYPL6 | protein | 730 | 4% helix, 43% strand | A0A1Y4JW59 |
| D | BCALYPL6 | protein | 730 | 4% helix, 42% strand | A0A1Y4JW59 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MLI · Malonate ion · additive · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.67 | 0.83 | 36 | empty |
| 2 | 316 | 0.66 | 0.81 | 41 | empty |
| 3 | 332 | 0.65 | 0.80 | 40 | empty |
| 4 | 205 | 0.58 | 0.80 | 32 | empty |
| 5 | 332 | 0.55 | 0.75 | 45 | empty |
Interfaces
5 interfaces between chains.
- A–B · 416 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 395 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 194 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 127 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DMK · PL6 alginate lyase BcAlyPL6 · 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 A0A1Y4JW59
- Elsewhere: RCSB PDB 7DMK · PDBe 7DMK · UniProt A0A1Y4JW59
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