Research workbench
Native-crystal structure of three chain non-toxic type II ribosome inactivating protein purified from the seeds of trichosanthes anguina
Analyse Native-crystal structure of three chain non-toxic type II ribosome inactivating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y42
- Type
- protein
- Length
- 1,022 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin; Seed lectin
- UniProt
- U3KRF6, U3KRF8
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Lectin | protein | 41 | 37% helix, 34% strand | U3KRF6 |
| B, E | Seed lectin | protein | 206 | 40% helix, 24% strand | U3KRF8 |
| C, F | Seed lectin | protein | 264 | 12% helix, 41% strand | U3KRF8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 23 | empty |
| 2 | 118 | 0.79 | 0.98 | 24 | empty |
| 3 | 1037 | 0.79 | 0.81 | 108 | empty |
| 4 | 375 | 0.59 | 0.76 | 42 | empty |
| 5 | 321 | 0.58 | 0.77 | 36 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1756 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1739 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1731 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1725 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 461 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5Y42 · Native-crystal structure of three chain non-toxic type II ribosome inactivating protein… · the same entry in another collection · chain F against F, TM-score 1.00
- U3KRF8 · AlphaFold monomer V2.0 prediction for seed lectin (U3KRF8) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 U3KRF6
- Every structure of UniProt U3KRF8
- Elsewhere: RCSB PDB 5Y42 · PDBe 5Y42 · UniProt U3KRF6 · UniProt U3KRF8
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