Research workbench
Crystal structure of ostrinia furnacalis group II chitinase catalytic domain 2 E2180L mutant in complex with penta-N-acetylchitooctaose (NAG)5
Analyse Crystal structure of ostrinia furnacalis group II chitinase catalytic domain 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y2C
- Type
- protein
- Length
- 766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insect group II chitinase
- Ligands
- NAG, MAN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Insect group II chitinase | protein | 383 | 36% helix, 22% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.74 | 0.81 | 62 | NAG |
| 2 | 386 | 0.71 | 0.82 | 50 | NAG |
| 3 | 260 | 0.65 | 0.83 | 41 | empty |
| 4 | 164 | 0.58 | 0.82 | 28 | empty |
| 5 | 68 | 0.52 | 0.86 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1083 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y2C · Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 2 E2180L… · 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
- Elsewhere: RCSB PDB 5Y2C · PDBe 5Y2C
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