MolNFT v1 · #140174 · protein
Crystal structure of ostrinia furnacalis group II chitinase catalytic domain 2
5Y2A · Insect group II chitinase: “Crystal structure of ostrinia furnacalis group II chitinase catalytic domain 2”. X-ray diffraction, 2 ligands (MAN, NAG), 5 pockets (best druggability 0.80). MolNFT v1 #140174 on GenesisL1: 3D structure…
- PDB
- 5Y2A
- Type
- protein
- Length
- 766 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insect group II chitinase
- EC
- 3.2.1.14
- Ligands
- MAN, NAG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Insect group II chitinase (EC 3.2.1.14) | protein | 383 | 36% helix, 21% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 8 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.80 | 0.81 | 106 | empty |
| 2 | 267 | 0.66 | 0.83 | 44 | empty |
| 3 | 165 | 0.56 | 0.81 | 28 | empty |
| 4 | 75 | 0.54 | 0.86 | 16 | empty |
| 5 | 73 | 0.51 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1043 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5Y2A · Crystal structure of Ostrinia furnacalis Group II chitinase catalytic domain 2 · 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 5Y2A · PDBe 5Y2A
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