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Crystal structure of a glycosylated beta-1,3-glucanase (hev B 2), an allergen from hevea brasiliensis (space group P41)
Analyse Crystal structure of a glycosylated beta-1,3-glucanase (hev B 2), an allergen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IIS
- Type
- protein
- Length
- 1,264 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-1,3-glucanase form 'rrii gln 2'
- EC
- 3.2.1.39
- UniProt
- D1M8S7
- Ligands
- NAG, NA
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-1,3-glucanase form 'rrii gln 2' (EC 3.2.1.39) | protein | 316 | 39% helix, 16% strand | D1M8S7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains C
- NA · Sodium ion · metal · chains C
- FLC · Citrate anion · additive · 3 copies · chains A, D
- CAC · Cacodylate ion · additive · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.82 | 0.84 | 109 | NA |
| 2 | 1093 | 0.82 | 0.83 | 126 | FLC |
| 3 | 211 | 0.50 | 0.76 | 25 | empty |
| 4 | 202 | 0.47 | 0.75 | 22 | empty |
| 5 | 77 | 0.39 | 0.78 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1420 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1325 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 480 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 472 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 glycan (cyclization, N-glycosylation).
Compared structures
- 4IIS · Crystal structure of a glycosylated beta-1,3-glucanase (HEV B 2), An allergen from Hevea… · 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 D1M8S7
- Elsewhere: RCSB PDB 4IIS · PDBe 4IIS · UniProt D1M8S7
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