Research workbench
Crystal structure of acmnpv chitinase a in complex with chitotrio- thiazoline dithioamide
Analyse Crystal structure of acmnpv chitinase a in complex with chitotrio- thiazoline… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DF0
- Type
- protein
- Length
- 1,056 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ac-chia
- EC
- 3.2.1.14
- UniProt
- Q70SQ1
- Ligands
- SN5, 58Y, NAG, SO4, CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ac-chia (EC 3.2.1.14) | protein | 528 | 26% helix, 26% strand | Q70SQ1 |
Ligands and binding sites
- SN5 · 2-deoxy-2-(ethanethioylamino)-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- 58Y · (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 825 | 0.79 | 0.83 | 72 | empty |
| 2 | 401 | 0.71 | 0.83 | 48 | NAG |
| 3 | 512 | 0.71 | 0.80 | 49 | NAG, SN5, 58Y |
| 4 | 557 | 0.70 | 0.79 | 52 | NAG, SN5, 58Y |
| 5 | 127 | 0.45 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1232 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5DF0 · Crystal structure of AcMNPV Chitinase A in complex WITH CHITOTRIO-THIAZOLINE DITHIOAMIDE · 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
- Every structure of UniProt Q70SQ1
- Elsewhere: RCSB PDB 5DF0 · PDBe 5DF0 · UniProt Q70SQ1
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