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Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor
Analyse Crystal structure of plant cell wall invertase in complex with a specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XQR
- Type
- protein
- Length
- 4,098 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-fructofuranosidase, insoluble isoenzyme CWINV1; Invertase inhibitor
- EC
- 3.2.1.26
- UniProt
- Q43866, O49908
- Ligands
- NAG, BMA, MAN, FRU, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Beta-fructofuranosidase, insoluble isoenzyme CWINV1 (EC 3.2.1.26) | protein | 537 | 6% helix, 47% strand | Q43866 |
| B, D, F, H, J, L | Invertase inhibitor | protein | 146 | 79% helix, 0% strand | O49908 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, C, E, G, I, K
- MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, C, E, G, I, K
- FRU · beta-D-fructofuranose · sugar · 6 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, E, C, G, I, K
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains B, D, F, H, J, K, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.78 | 0.80 | 87 | EPE |
| 2 | 676 | 0.70 | 0.78 | 75 | empty |
| 3 | 426 | 0.69 | 0.81 | 43 | NAG |
| 4 | 431 | 0.68 | 0.80 | 45 | NAG |
| 5 | 436 | 0.67 | 0.79 | 42 | NAG |
Interfaces
15 interfaces between chains.
- E–F · 1087 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1075 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 1067 Ų buried · 21 hydrogen bonds · protein-protein
- K–L · 1062 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 2XQR · Crystal structure of plant cell wall invertase in complex with a specific protein… · the same entry in another collection · chain L against L, 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 Q43866
- Every structure of UniProt O49908
- Elsewhere: RCSB PDB 2XQR · PDBe 2XQR · UniProt Q43866 · UniProt O49908
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