Research workbench
Crystal structure of the complex formed between type I ribosome inactivating protein and hexapeptide ser-asp-asp-asp-met-gly at 1.7 a resolution
Analyse Crystal structure of the complex formed between type I ribosome inactivating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N3X
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome inactivating protein; Sdddmg peptide
- EC
- 3.2.2.22
- Ligands
- GUN, NAG
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosome inactivating protein (EC 3.2.2.22) | protein | 246 | 42% helix, 25% strand | — |
| B | Sdddmg peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- GUN · Guanine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.48 | 0.78 | 18 | GUN |
Interfaces
1 interface between chains.
- A–B · 516 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 3N3X · Crystal Structure of the complex formed between type I ribosome inactivating protein and… · 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
- Elsewhere: RCSB PDB 3N3X · PDBe 3N3X
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