Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-phenylalanyl-N6-((benzyloxy)carbonyl)-L-lysine. Determined by X-ray diffraction at 1.45 Å resolution. Released 16 Nov 2022.
Explore 7Y4M in 3D Show helices and sheets RCSB PDB PDBe
7Y4M contains 18 α-helices and 17 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 8-12 | 5 | 1 |
| α-helix | 18-32 | 15 | |
| β-strand | 38-39 | 2 | 2 |
| β-strand | 42-43 | 2 | 2 |
| β-strand | 44 | 1 | 3 |
| α-helix | 45-47 | 3 | |
| α-helix | 53-55 | 3 | |
| β-strand | 57-63 | 7 | 1 |
| β-strand | 69-75 | 7 | 1 |
| β-strand | 80-86 | 7 | 1 |
| β-strand | 89-92 | 4 | 1 |
| α-helix | 93-95 | 3 | |
| α-helix | 98-103 | 6 | |
| α-helix | 104-106 | 3 | |
| β-strand | 113-116 | 4 | 1 |
| α-helix | 123-130 | 8 | |
| α-helix | 134-136 | 3 | |
| β-strand | 139 | 1 | 4 |
| α-helix | 141-152 | 12 | |
| α-helix | 154-156 | 3 | |
| α-helix | 161-172 | 12 | |
| α-helix | 173-177 | 5 | |
| α-helix | 178-180 | 3 | |
| β-strand | 181 | 1 | 5 |
| α-helix | 182-194 | 13 | |
| β-strand | 198 | 1 | 4 |
| α-helix | 199-201 | 3 | |
| α-helix | 202-220 | 19 | |
| β-strand | 222 | 1 | 6 |
| β-strand | 225-233 | 9 | 6 |
| β-strand | 239-244 | 6 | 6 |
| α-helix | 245-248 | 4 | |
| β-strand | 252 | 1 | 5 |
| β-strand | 255 | 1 | 3 |
| α-helix | 260-263 | 4 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ricin A chain | A | protein | 274 | Ricinus communis | P02879 (AlphaFold model) |
>7Y4M_1 Ricin A chain (chains A) MHHHHHHIFPKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPI NQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQN RYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQ MISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQ RRNGSKFSVYDVSILIPIIALMVYRCAPPPSSQF
| ID | Name | Formula | Copies |
|---|---|---|---|
| IWQ | (2S)-2-[[(2S)-2-[2-[(2-azanyl-4-oxidanylidene-3H-pteridin-7-yl)carbonylamino]et… | C32 H35 N9 O8 | 1 |
Water and common crystallization additives (SO4) are not listed.
Pterin-based small molecule inhibitor capable of binding to the secondary pocket in the active site of ricin-toxin A chain. Saito, R., Goto, M., Katakura, S. et al. PLoS One (2022) 17:e0277770-e0277770. DOI 10.1371/journal.pone.0277770 · PubMed
Other PDB entries of the same protein (UniProt P02879 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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