MolNFT v1 · #106759 · protein
Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity
4TOQ: “Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity”. X-ray diffraction, 2 ligands (MG, CL), 9 pockets (best druggability 0.78). MolNFT v1 #106759 on GenesisL1: 3D…
- 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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