Research workbench
Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity
Analyse Crystal structure of class III chitinase from pomegranate provides the insight… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TOQ
- Type
- protein
- Length
- 1,089 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Class III chitinase
- EC
- 3.2.1.14
- UniProt
- G1UH28
- Ligands
- MG, CL
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Class III chitinase (EC 3.2.1.14) | protein | 273 | 32% helix, 23% strand | G1UH28 |
| B | Class III chitinase (EC 3.2.1.14) | protein | 270 | 32% helix, 21% strand | G1UH28 |
Ligands and binding sites
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.78 | 0.80 | 87 | CL, MG |
| 2 | 928 | 0.73 | 0.78 | 78 | empty |
| 3 | 903 | 0.72 | 0.77 | 66 | empty |
| 4 | 783 | 0.71 | 0.77 | 60 | empty |
| 5 | 75 | 0.34 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 441 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 402 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 379 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 235 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4TOQ · Crystal structure of class III chitinase from pomegranate provides the insight into its… · the same entry in another collection · chain D against D, TM-score 1.00
- G1UH28 · AlphaFold monomer V2.0 prediction for acidic endochitinase pun G 14, amyloplastic (G1UH28) · 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 G1UH28
- Elsewhere: RCSB PDB 4TOQ · PDBe 4TOQ · UniProt G1UH28
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