Research workbench
Open and closed conformations and protonation states of candida antarctica lipase B: xenon complex
Analyse Open and closed conformations and protonation states of candida antarctica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6V
- Type
- protein
- Length
- 633 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
- NAG, XE
- Pockets
- 1 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipase B (EC 3.1.1.3) | protein | 317 | 39% helix, 16% strand | P41365 |
| B | Lipase B (EC 3.1.1.3) | protein | 316 | 36% helix, 16% strand | P41365 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- XE · Xenon · ion · 6 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1108 | 0.80 | 0.81 | 121 | IPA, XE |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5A6V · Open and closed conformations and protonation states of Candida antarctica Lipase B… · 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 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 P41365
- Elsewhere: RCSB PDB 5A6V · PDBe 5A6V · UniProt P41365
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