1ZKK: PDB entry 1ZKK
Crystal structure of hSET8 in ternary complex with H4 peptide (16-24) and AdoHcy. Determined by X-ray diffraction at 1.45 Å resolution. Released 7 Jun 2005.
- Method
- X-ray diffraction
- Resolution
- 1.45 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 6,545
- Mol. weight
- 82.19 kDa
- Ligands
- SAH
- Released
- 7 Jun 2005
Explore 1ZKK in 3D
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RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1ZKK contains 30 α-helices and 56 β-strands across 8 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.
Chain A: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-212 | 18 | |
| β-strand | 218-223 | 6 | 1 |
| β-strand | 227-232 | 6 | 1 |
| β-strand | 236 | 1 | 2 |
| β-strand | 241-245 | 5 | 3 |
| β-strand | 248-251 | 4 | 4 |
| α-helix | 252-262 | 11 | |
| β-strand | 272-277 | 6 | 4 |
| β-strand | 280-285 | 6 | 4 |
| α-helix | 294-296 | 3 | |
| β-strand | 298-299 | 2 | 5 |
| β-strand | 305-312 | 8 | 3 |
| β-strand | 315-322 | 8 | 3 |
| β-strand | 326 | 1 | 2 |
| α-helix | 330 | 1 | |
| β-strand | 331 | 1 | 1 |
| α-helix | 332 | 1 | |
| β-strand | 333-334 | 2 | 5 |
| α-helix | 341-346 | 6 | |
| α-helix | 348-351 | 4 | |
Chain B: 7 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-212 | 18 | |
| β-strand | 218-223 | 6 | 6 |
| β-strand | 227-232 | 6 | 6 |
| β-strand | 236 | 1 | 7 |
| β-strand | 241-244 | 4 | 8 |
| β-strand | 248-251 | 4 | 9 |
| α-helix | 252-262 | 11 | |
| β-strand | 272-277 | 6 | 9 |
| β-strand | 280-285 | 6 | 9 |
| α-helix | 294-296 | 3 | |
| β-strand | 298-299 | 2 | 10 |
| β-strand | 305-312 | 8 | 8 |
| β-strand | 315-322 | 8 | 8 |
| β-strand | 326 | 1 | 7 |
| α-helix | 330 | 1 | |
| β-strand | 331 | 1 | 6 |
| α-helix | 332 | 1 | |
| β-strand | 333-334 | 2 | 10 |
| α-helix | 341-346 | 6 | |
| α-helix | 348-351 | 4 | |
Chain C: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-212 | 18 | |
| β-strand | 218-223 | 6 | 11 |
| β-strand | 227-232 | 6 | 11 |
| β-strand | 236 | 1 | 12 |
| β-strand | 241-244 | 4 | 13 |
| β-strand | 248-251 | 4 | 14 |
| α-helix | 252-262 | 11 | |
| β-strand | 272-277 | 6 | 14 |
| β-strand | 280-285 | 6 | 14 |
| α-helix | 294-296 | 3 | |
| α-helix | 297 | 1 | |
| β-strand | 298-299 | 2 | 15 |
| β-strand | 305-312 | 8 | 13 |
| β-strand | 315-322 | 8 | 13 |
| β-strand | 326 | 1 | 12 |
| α-helix | 330 | 1 | |
| β-strand | 331 | 1 | 11 |
| α-helix | 332 | 1 | |
| β-strand | 333-334 | 2 | 15 |
| α-helix | 341-346 | 6 | |
| α-helix | 348-351 | 4 | |
Chain D: 8 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 195-212 | 18 | |
| β-strand | 218-223 | 6 | 16 |
| β-strand | 227-232 | 6 | 16 |
| β-strand | 236 | 1 | 17 |
| β-strand | 241-245 | 5 | 18 |
| β-strand | 248-251 | 4 | 19 |
| α-helix | 252-262 | 11 | |
| β-strand | 272-277 | 6 | 19 |
| β-strand | 280-285 | 6 | 19 |
| α-helix | 294-296 | 3 | |
| α-helix | 297 | 1 | |
| β-strand | 298-299 | 2 | 18 |
| β-strand | 305-312 | 8 | 18 |
| β-strand | 315-322 | 8 | 18 |
| β-strand | 326 | 1 | 17 |
| α-helix | 330 | 1 | |
| β-strand | 331 | 1 | 16 |
| α-helix | 332 | 1 | |
| β-strand | 333-334 | 2 | 18 |
| α-helix | 341-346 | 6 | |
| α-helix | 348-351 | 4 | |
Chains E, F, G and H: 0 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| β-strand | 20-21 | 2 | 4 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone-lysine N-methyltransferase, H4 lysine-20 specific | A, B, C, D | protein | 167 | Homo sapiens | Q9NQR1 (AlphaFold model) |
| Peptide corresponding to residues 15-24 of histone H4 | E, F, G, H | protein | 10 | | P62805 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>1ZKK_1 Histone-lysine N-methyltransferase, H4 lysine-20 specific (chains A, B, C, D)
GAMGSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEY
HGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNC
QTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH
Sequence of entity 2 (E, F, G, H), FASTA
>1ZKK_2 Peptide corresponding to residues 15-24 of histone H4 (chains E, F, G, H)
AKRHRKVLRD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SAH | S-adenosyl-L-homocysteine | C14 H20 N6 O5 S | 4 |
Primary citation
Structural and functional analysis of SET8, a histone H4 Lys-20 methyltransferase. Couture, J.-F., Collazo, E., Brunzelle, J.S. et al. Genes Dev (2005) 19:1455-1465. DOI 10.1101/gad.1318405 · PubMed
Other PDB entries of the same protein (UniProt Q9NQR1 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3F9X 1.25 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
- 5TEG 1.3 Å, Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and…
- 2BQZ 1.5 Å, Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7…
- 3F9Y 1.5 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
- 3F9W 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
- 3F9Z 1.6 Å, Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases,…
- 5W1Y 1.7 Å, SETD8 in complex with a covalent inhibitor
- 5TH7 1.95 Å, Complex of SETD8 with MS453
- 4IJ8 2.0 Å, Crystal structure of the complex of SETD8 with SAM
- 5V2N 2.0 Å, Crystal Structure of APO Human SETD8
- 9CR7 2.05 Å, Structure of human SETD8 in complex with covalent inhibitor AM2928
- 5T5G 2.1 Å, human SETD8 in complex with MS2177
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