Research workbench
The acidic mammalian chitinase catalytic domain in complex with methylallosamidin
Analyse The acidic mammalian chitinase catalytic domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FY1
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidic mammalian chitinase
- EC
- 3.2.1.14
- UniProt
- Q9BZP6
- Ligands
- NA1, AMI, NAA
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acidic mammalian chitinase (EC 3.2.1.14) | protein | 377 | 38% helix, 22% strand | Q9BZP6 |
| B | Acidic mammalian chitinase (EC 3.2.1.14) | protein | 373 | 38% helix, 23% strand | Q9BZP6 |
Ligands and binding sites
- NA1 · 2-acetamido-2-deoxy-6-O-methyl-alpha-D-allopyranose · ligand · 2 copies · chains A, B
- AMI · Allosamizoline · ligand · 2 copies · chains A, B
- NAA · 2-acetamido-2-deoxy-beta-D-allopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.69 | 0.83 | 60 | NAA, AMI |
| 2 | 225 | 0.66 | 0.83 | 42 | NAA, AMI |
| 3 | 212 | 0.62 | 0.82 | 21 | NA1 |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3FY1 · The Acidic Mammalian Chitinase catalytic domain in complex with methylallosamidin · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BZP6 · AlphaFold monomer V2.0 prediction for acidic mammalian chitinase (Q9BZP6) · 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 Q9BZP6
- Elsewhere: RCSB PDB 3FY1 · PDBe 3FY1 · UniProt Q9BZP6
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