Ricin A chain bound to camelid nanobody (VHH2)(F5). Determined by X-ray diffraction at 1.5 Å resolution. Released 20 Jul 2016.
Explore 4Z9K in 3D Show helices and sheets RCSB PDB PDBe
4Z9K contains 16 α-helices and 27 β-strands across 2 chains. 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 | 9-13 | 5 | 1 |
| α-helix | 19-33 | 15 | |
| β-strand | 39-40 | 2 | 2 |
| β-strand | 43-44 | 2 | 2 |
| β-strand | 45 | 1 | 3 |
| α-helix | 46-48 | 3 | |
| α-helix | 54-56 | 3 | |
| β-strand | 58-64 | 7 | 1 |
| β-strand | 70-76 | 7 | 1 |
| β-strand | 82-87 | 6 | 1 |
| β-strand | 90-93 | 4 | 1 |
| α-helix | 94-96 | 3 | |
| α-helix | 99-105 | 7 | |
| β-strand | 114-117 | 4 | 1 |
| β-strand | 118 | 1 | 4 |
| α-helix | 124-131 | 8 | |
| α-helix | 135-137 | 3 | |
| β-strand | 140 | 1 | 5 |
| α-helix | 142-155 | 14 | |
| α-helix | 162-172 | 11 | |
| α-helix | 173-178 | 6 | |
| α-helix | 179-181 | 3 | |
| α-helix | 183-194 | 12 | |
| β-strand | 199 | 1 | 5 |
| α-helix | 203-220 | 18 | |
| β-strand | 223 | 1 | 6 |
| β-strand | 226-234 | 9 | 6 |
| β-strand | 240-245 | 6 | 6 |
| α-helix | 246-249 | 4 | |
| β-strand | 256 | 1 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 5-7 | 3 | 7 |
| β-strand | 10-11 | 2 | 8 |
| β-strand | 18-23 | 6 | 7 |
| β-strand | 32 | 1 | 4 |
| β-strand | 34-39 | 6 | 8 |
| β-strand | 46-52 | 7 | 8 |
| β-strand | 55-58 | 4 | 8 |
| α-helix | 60-62 | 3 | |
| β-strand | 66-71 | 6 | 7 |
| β-strand | 74-79 | 6 | 7 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-93 | 6 | 8 |
| β-strand | 113-116 | 4 | 8 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ricin | A | protein | 258 | Ricinus communis | P02879 (AlphaFold model) |
| VHH2(F5) antibody | B | protein | 116 | Vicugna pacos |
>4Z9K_1 Ricin (chains A) KQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELS NHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNY DRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQY IEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVY DVSILIPIIALMVYRCAP
>4Z9K_2 VHH2(F5) antibody (chains B) VQLVESGGGLVQPGGSLRLSCAASGFTLDDYAIGWFRQVPGKEREGVACVKDGSTYYADS VKGRFTISRDNGAVYLQMNSLKPEDTAVYYCASRPCFLGVPLIDFGSWGQGTQVTV
| ID | Name | Formula | Copies |
|---|---|---|---|
| ZN | Zinc ion | Zn | 1 |
Water and common crystallization additives (CL, EDO) are not listed.
Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit. Rudolph, M.J., Vance, D.J., Cassidy, M.S. et al. Proteins (2016) 84:1162-1172. DOI 10.1002/prot.25062 · 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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