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Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose
Analyse Crystal structure of the N-glycan-deficient variant N448A of isopullulanase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WWG
- Type
- protein
- Length
- 2,159 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopullulanase
- EC
- 3.2.1.57
- UniProt
- O00105
- Ligands
- NAG, GLC, BGC
- Pockets
- 20 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopullulanase (EC 3.2.1.57) | protein | 536 | 6% helix, 46% strand | O00105 |
| B | Isopullulanase (EC 3.2.1.57) | protein | 542 | 6% helix, 46% strand | O00105 |
| C | Isopullulanase (EC 3.2.1.57) | protein | 541 | 5% helix, 46% strand | O00105 |
| D | Isopullulanase (EC 3.2.1.57) | protein | 540 | 5% helix, 46% strand | O00105 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains B, C
- BGC · beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.54 | 0.74 | 40 | GLC |
| 2 | 265 | 0.50 | 0.75 | 33 | NAG |
| 3 | 259 | 0.49 | 0.74 | 35 | empty |
| 4 | 226 | 0.46 | 0.74 | 24 | NAG |
| 5 | 192 | 0.44 | 0.74 | 20 | BGC, GLC |
Interfaces
4 interfaces between chains.
- C–D · 361 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 355 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 87 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 74 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 glycan (N-glycosylation).
Compared structures
- 3WWG · Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed… · the same entry in another collection · chain D against D, TM-score 1.00
- O00105 · AlphaFold monomer V2.0 prediction for isopullulanase (O00105) · 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 O00105
- Elsewhere: RCSB PDB 3WWG · PDBe 3WWG · UniProt O00105
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