Structure of PDB 5kfm Chain A

Receptor sequence

>5kfmA (length=427) Species: 9606 (Homo sapiens)

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLPISADLLPSTYIEGL
PQGPTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIE
RETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKI
RSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGI
EHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKD
RNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKN
CNTSGIQTEWSPPLTMLFLCATKFSAS

3D structure

• PDB: 5kfm Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	Q38 Y39 W42 R61 S62 W64 K86 R93 K293 R313 P316 K317 T318 G320 C321 S322 K323 N324 P326 R351	Q41 Y42 W45 R64 S65 W67 K89 R96 K288 R308 P311 K312 T313 G315 C316 S317 K318 N319 P321 R346
BS02	dna	A	S113 E116 K224 S257 G259 G260 K261 L262 R377 L381 R382 C384	S116 E119 K219 S252 G254 G255 K256 L257 R372 L376 R377 C379
BS03	CA	A	D13 M14 D115	D16 M17 D118
BS04	STP	A	M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231	M17 D18 C19 F20 F21 I51 Y55 R58 R64 D118 K226

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5kfm, PDBe:5kfm, PDBj:5kfm
• PDBsum: 5kfm
• PubMed: 27284197
• UniProt: Q9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)