Research workbench
Crystal structure analysis of the trichosanthin delta C7
Analyse Crystal structure analysis of the trichosanthin delta C7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J4G
- Type
- protein
- Length
- 964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichosanthin delta C7
- EC
- 3.2.2.22
- UniProt
- P09989
- Ligands
- CA
- Pockets
- 11 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Trichosanthin delta C7 (EC 3.2.2.22) | protein | 241 | 41% helix, 25% strand | P09989 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.51 | 0.74 | 45 | empty |
| 2 | 242 | 0.50 | 0.75 | 40 | empty |
| 3 | 189 | 0.47 | 0.75 | 34 | CA |
| 4 | 129 | 0.45 | 0.77 | 26 | CA |
| 5 | 174 | 0.45 | 0.75 | 31 | CA |
Interfaces
2 interfaces between chains.
- A–B · 459 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 431 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1J4G · crystal structure analysis of the trichosanthin delta C7 · 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 1J4G · PDBe 1J4G · UniProt P09989
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