Research workbench
Hydroxynitrile lyase from the millipede, chamberlinius hualienensis, complexed with iodoacetate
Analyse Hydroxynitrile lyase from the millipede, chamberlinius hualienensis, complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KFD
- Type
- protein
- Length
- 162 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxynitrile lyase
- UniProt
- A0A0H5BR52
- Ligands
- 04E, NAG
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxynitrile lyase | protein | 162 | 15% helix, 41% strand | A0A0H5BR52 |
Ligands and binding sites
- 04E · iodoacetic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.62 | 0.88 | 22 | 04E |
| 2 | 51 | 0.39 | 0.81 | 13 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6KFD · Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis, complexed with… · 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 A0A0H5BR52
- Elsewhere: RCSB PDB 6KFD · PDBe 6KFD · UniProt A0A0H5BR52
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