Research workbench
Crystal structure of candida antarctica lipase B mutant sr with product analogue
Analyse Crystal structure of candida antarctica lipase B mutant sr with product analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J1T
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase B
- EC
- 3.1.1.3
- UniProt
- P41365
- Ligands
- B7U, CL, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase B (EC 3.1.1.3) | protein | 318 | 36% helix, 16% strand | P41365 |
Ligands and binding sites
- B7U · (2S)-2-phenyl-N-[(1R)-1-phenylethyl]propanamide · ligand · chains A
- CL · Chloride ion · ion · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.60 | 0.81 | 26 | CL |
| 2 | 205 | 0.58 | 0.80 | 27 | B7U |
| 3 | 173 | 0.50 | 0.77 | 23 | EDO |
| 4 | 71 | 0.34 | 0.76 | 19 | empty |
| 5 | 60 | 0.33 | 0.77 | 14 | PEG |
Interfaces
1 interface between chains.
- A–B · 679 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6J1T · Crystal structure of Candida Antarctica Lipase B mutant SR with product analogue · the same entry in another collection · chain A against A, TM-score 1.00
- P41365 · AlphaFold monomer V2.0 prediction for lipase B (P41365) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P41365
- Elsewhere: RCSB PDB 6J1T · PDBe 6J1T · UniProt P41365
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