Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 1 mM Mg2+ for 1800s. Determined by X-ray diffraction at 1.45 Å resolution. Released 22 Jun 2016.
Explore 5KFN in 3D Show helices and sheets RCSB PDB PDBe
5KFN contains 23 α-helices and 20 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 | 9-14 | 6 | 1 |
| α-helix | 17-25 | 9 | |
| α-helix | 27-29 | 3 | |
| β-strand | 34-38 | 5 | 2 |
| β-strand | 46-50 | 5 | 2 |
| α-helix | 52-55 | 4 | |
| β-strand | 64 | 1 | 2 |
| α-helix | 65-71 | 7 | |
| β-strand | 76-79 | 4 | 2 |
| α-helix | 80-81 | 2 | |
| β-strand | 82-83 | 2 | 3 |
| β-strand | 86-87 | 2 | 3 |
| α-helix | 90-106 | 17 | |
| β-strand | 109-113 | 5 | 1 |
| β-strand | 116-120 | 5 | 1 |
| α-helix | 122-132 | 11 | |
| α-helix | 135-138 | 4 | |
| α-helix | 139-141 | 3 | |
| β-strand | 145-147 | 3 | 1 |
| α-helix | 163-177 | 15 | |
| α-helix | 186-208 | 23 | |
| β-strand | 212-217 | 6 | 1 |
| α-helix | 220-227 | 8 | |
| β-strand | 235-237 | 3 | 1 |
| α-helix | 240-242 | 3 | |
| α-helix | 243-248 | 6 | |
| β-strand | 251 | 1 | 4 |
| α-helix | 252-254 | 3 | |
| α-helix | 261-270 | 10 | |
| β-strand | 274 | 1 | 4 |
| α-helix | 275-280 | 6 | |
| α-helix | 283-290 | 8 | |
| α-helix | 292-301 | 10 | |
| β-strand | 313 | 1 | 1 |
| β-strand | 319-324 | 6 | 5 |
| α-helix | 327-329 | 3 | |
| β-strand | 331-333 | 3 | 5 |
| α-helix | 334-359 | 26 | |
| β-strand | 361-372 | 12 | 5 |
| β-strand | 381-386 | 6 | 5 |
| α-helix | 392-403 | 12 | |
| α-helix | 404-406 | 3 | |
| β-strand | 414-431 | 18 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| DNA polymerase eta | A | protein | 435 | Homo sapiens | Q9Y253 (AlphaFold model) |
| DNA (5'-d(*cp*ap*tp*tp*ap*tp*gp*ap*cp*gp*cp*t)-3') | T | DNA | 12 | Homo sapiens | |
| DNA (5'-d(*ap*gp*cp*gp*tp*cp*ap*t)-3') | P | DNA | 8 | Homo sapiens |
>5KFN_1 DNA polymerase eta (chains A) GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAF GVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEA YVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDS LQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTL VSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSW LYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRN DNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSP PLTMLFLCATKFSAS
>5KFN_2 DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') (chains T) CATTATGACGCT
>5KFN_3 DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3') (chains P) AGCGTCAT
| ID | Name | Formula | Copies |
|---|---|---|---|
| STP | 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) | C10 H16 N5 O11 P3 S | 1 |
| CA | Calcium ion | Ca | 1 |
| MG | Magnesium ion | Mg | 3 |
Water and common crystallization additives (GOL) are not listed.
Capture of a third Mg2+ is essential for catalyzing DNA synthesis. Gao, Y., Yang, W. Science (2016) 352:1334-1337. DOI 10.1126/science.aad9633 · PubMed
Other PDB entries of the same protein (UniProt Q9Y253 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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