Research workbench
Structure of a circular permutation on lipase B from candida antartica with bound suicide inhibitor
Analyse Structure of a circular permutation on lipase B from candida antartica with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICW
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase B
- EC
- 3.1.1.3
- UniProt
- P41365
- Ligands
- MHH, NAG, PO4
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase B (EC 3.1.1.3) | protein | 291 | 32% helix, 16% strand | P41365 |
Ligands and binding sites
- MHH · methyl hydrogen (R)-hexylphosphonate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.34 | 0.77 | 15 | MHH |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3ICW · Structure of a Circular Permutation on Lipase B from Candida Antartica with Bound Suicide… · 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 0.92
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 3ICW · PDBe 3ICW · UniProt P41365
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