Research workbench
Crystal structure of aspergillus fumigatus lipase B
Analyse Crystal structure of aspergillus fumigatus lipase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IDY
- Type
- protein
- Length
- 1,260 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase aflb
- UniProt
- A0A229Y729
- Ligands
- CA, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase aflb | protein | 421 | 45% helix, 10% strand | A0A229Y729 |
| B | Lipase aflb | protein | 420 | 44% helix, 10% strand | A0A229Y729 |
| C | Lipase aflb | protein | 419 | 43% helix, 10% strand | A0A229Y729 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.72 | 0.76 | 93 | empty |
| 2 | 525 | 0.60 | 0.74 | 41 | SO4 |
| 3 | 339 | 0.59 | 0.77 | 49 | empty |
| 4 | 157 | 0.55 | 0.81 | 20 | empty |
| 5 | 111 | 0.43 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1244 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 362 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 83 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6IDY · Crystal structure of Aspergillus fumigatus lipase B · 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 A0A229Y729
- Elsewhere: RCSB PDB 6IDY · PDBe 6IDY · UniProt A0A229Y729
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