Research workbench
Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin
Analyse Structure of C-terminal region of acidic P2 ribosomal protein complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JDL
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosome-inactivating protein alpha-trichosanthin; Acidic ribosomal protein P2
- EC
- 3.2.2.22
- UniProt
- P09989
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosome-inactivating protein alpha-trichosanthin (EC 3.2.2.22) | protein | 247 | 39% helix, 25% strand | P09989 |
| C | Acidic ribosomal protein P2 | protein | 10 | 0% helix, 0% strand | — |
| D | Acidic ribosomal protein P2 | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.52 | 0.74 | 56 | empty |
| 2 | 90 | 0.45 | 0.80 | 18 | empty |
| 3 | 100 | 0.42 | 0.77 | 21 | empty |
| 4 | 59 | 0.26 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 589 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 542 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 223 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2JDL · Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin · the same entry in another collection · chain A against A, TM-score 1.00
- P09989 · AlphaFold monomer V2.0 prediction for ribosome-inactivating protein alpha-trichosanthin… · a predicted model of the same protein · chain A 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 P09989
- Elsewhere: RCSB PDB 2JDL · PDBe 2JDL · UniProt P09989
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.