MolNFT v1 · #55164 · protein
Crystal structure of human acidic chitinase in complex with bisdionin C
2YBT · Acidic mammalian chitinase: “Crystal structure of human acidic chitinase in complex with bisdionin C”. X-ray diffraction, 1 ligand (DW0), 20 pockets (best druggability 0.81). MolNFT v1 #55164 on GenesisL1: 3D structure, binding…
- PDB
- 2YBT
- Type
- protein
- Length
- 2,262 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acidic mammalian chitinase
- EC
- 3.2.1.14
- UniProt
- Q9BZP6
- Ligands
- DW0
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Acidic mammalian chitinase (EC 3.2.1.14) | protein | 377 | 36% helix, 22% strand | Q9BZP6 |
Ligands and binding sites
- DW0 · 1,1'-propane-1,3-diylbis(3,7-dimethyl-3,7-dihydro-1H-purine-2,6-dione) · ligand · 12 copies · chains A, D, B, F, C, E
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.81 | 0.82 | 101 | empty |
| 2 | 667 | 0.79 | 0.83 | 77 | GOL, DW0 |
| 3 | 612 | 0.77 | 0.83 | 79 | GOL, DW0 |
| 4 | 276 | 0.71 | 0.85 | 42 | empty |
| 5 | 673 | 0.69 | 0.76 | 73 | GOL, DW0 |
Interfaces
8 interfaces between chains.
- A–B · 646 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 638 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 616 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 516 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 511 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 2YBT · Crystal structure of human acidic chitinase in complex with bisdionin C · the same entry in another collection · chain F against F, TM-score 1.00
- Q9BZP6 · AlphaFold monomer V2.0 prediction for acidic mammalian chitinase (Q9BZP6) · a predicted model of the same protein · chain C 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 2YBT · PDBe 2YBT · UniProt Q9BZP6
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