Research workbench
Crystal structure of ricin A chain in complex with 5-mesitylthiophene-2-carboxylic acid
Analyse Crystal structure of ricin A chain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MLO
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.65
- Source
- Ricinus communis
- Molecule
- Ricin
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- ZJ7, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.65 · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 260 | 40% helix, 22% strand | P02879 |
| B | Ricin (EC 3.2.2.22) | protein | 258 | 41% helix, 22% strand | P02879 |
Ligands and binding sites
- ZJ7 · 5-(2,4,6-trimethylphenyl)thiophene-2-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.79 | 0.89 | 35 | ZJ7 |
| 2 | 434 | 0.64 | 0.78 | 56 | empty |
| 3 | 212 | 0.56 | 0.79 | 29 | empty |
| 4 | 230 | 0.54 | 0.77 | 36 | empty |
| 5 | 68 | 0.40 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7MLO · Crystal structure of ricin a chain in complex with 5-mesitylthiophene- 2-carboxylic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P02879 · AlphaFold monomer V2.0 prediction for ricin (P02879) · 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 P02879
- Elsewhere: RCSB PDB 7MLO · PDBe 7MLO · UniProt P02879
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