Research workbench
Structure of a cell wall invertase inhibitor from tobacco in complex with CD2+
Analyse Structure of a cell wall invertase inhibitor from tobacco in complex with CD2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RJ4
- Type
- protein
- Length
- 585 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Invertase inhibitor
- UniProt
- O49908
- Ligands
- CD
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Invertase inhibitor | protein | 147 | 79% helix, 0% strand | O49908 |
| B, C, D | Invertase inhibitor | protein | 146 | 81% helix, 0% strand | O49908 |
Ligands and binding sites
- CD · Cadmium ion · metal · 8 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.56 | 0.79 | 27 | CD, BTB |
| 2 | 257 | 0.53 | 0.76 | 43 | empty |
| 3 | 226 | 0.52 | 0.77 | 27 | CD |
| 4 | 85 | 0.50 | 0.83 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 717 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 703 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 607 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1RJ4 · Structure of a Cell Wall Invertase Inhibitor from Tobacco in Complex with Cd2+ · 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 O49908
- Elsewhere: RCSB PDB 1RJ4 · PDBe 1RJ4 · UniProt O49908
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