Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide. Determined by X-ray diffraction at 1.95 Å resolution. Released 19 Apr 2017.
Explore 5VAC in 3D Show helices and sheets RCSB PDB PDBe
5VAC contains 12 α-helices and 26 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 | 162 | 1 | 1 |
| α-helix | 170-186 | 17 | |
| β-strand | 190-191 | 2 | 2 |
| β-strand | 196 | 1 | 3 |
| β-strand | 198 | 1 | 4 |
| β-strand | 202 | 1 | 4 |
| α-helix | 204-206 | 3 | |
| α-helix | 209-211 | 3 | |
| β-strand | 212 | 1 | 5 |
| α-helix | 217 | 1 | |
| β-strand | 218 | 1 | 6 |
| α-helix | 219-220 | 2 | |
| α-helix | 221-236 | 16 | |
| β-strand | 242-247 | 6 | 7 |
| β-strand | 251-256 | 6 | 7 |
| β-strand | 260 | 1 | 8 |
| β-strand | 264 | 1 | 1 |
| β-strand | 265-268 | 4 | 6 |
| β-strand | 272-275 | 4 | 3 |
| α-helix | 276-278 | 3 | |
| β-strand | 287-291 | 5 | 3 |
| β-strand | 293 | 1 | 5 |
| α-helix | 296-298 | 3 | |
| β-strand | 300-303 | 4 | 3 |
| β-strand | 307-308 | 2 | 2 |
| α-helix | 310-313 | 4 | |
| β-strand | 315-316 | 2 | 9 |
| α-helix | 324-327 | 4 | |
| β-strand | 330-337 | 8 | 6 |
| β-strand | 340-347 | 8 | 6 |
| β-strand | 351 | 1 | 8 |
| α-helix | 355 | 1 | |
| β-strand | 356 | 1 | 7 |
| α-helix | 357 | 1 | |
| β-strand | 358-359 | 2 | 9 |
| β-strand | 362 | 1 | 10 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 26-27 | 2 | 3 |
| β-strand | 28 | 1 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Probable Histone-lysine N-methyltransferase ATXR5 | A | protein | 229 | Ricinus communis | B9RU15 (AlphaFold model) |
| Histone H3.2 | C | protein | 19 | Homo sapiens | Q71DI3 (AlphaFold model) |
>5VAC_1 Probable Histone-lysine N-methyltransferase ATXR5 (chains A) RRRSGSLVYQKRRRRLLPFVSSEDPAQRLKQMGTLASALTELQMEFSDDLTYSSGMAPRS ANQARFEEGGMQVLTKEDIETLEQCRAMCKRGDCPPLLVVFDSREGFTVEADGQIKDMTF IAEYTGDVDYIRNREHDDCDSMMTLLLAKDPSSSLVICPDKRGNIARFISGINNHTLDGK KKQNCKCVRYSVNGECRVFLVATRDIAKGERLYYDYNGYEHEYPTQHFV
>5VAC_2 Histone H3.2 (chains C) KQLATKAARKSAPATGGVK
| ID | Name | Formula | Copies |
|---|---|---|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 1 |
Water and common crystallization additives (DMS) are not listed.
Molecular basis for the methylation specificity of ATXR5 for histone H3. Bergamin, E., Sarvan, S., Malette, J. et al. Nucleic Acids Res (2017) 45:6375-6387. DOI 10.1093/nar/gkx224 · PubMed
Other PDB entries of the same protein (UniProt B9RU15 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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