Structure of PDB 5kfn Chain A

Receptor sequence

>5kfnA (length=428) Species: 9606 (Homo sapiens)

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAI
ERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRK
IRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRG
IEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTK
DRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIK
NCNTSGIQTEWSPPLTMLFLCATKFSAS

3D structure

• PDB: 5kfn Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
• Chain: A
• Resolution: 1.45 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 S62 K86 R93 P316 K317 T318 G320 S322 K323 N324 P326 G327 R351	Q41 Y42 W45 S65 K89 R96 P312 K313 T314 G316 S318 K319 N320 P322 G323 R347
BS02	dna	A	S113 E116 S257 G259 G260 K261 L262 R377 R382 C384	S116 E119 S253 G255 G256 K257 L258 R373 R378 C380
BS03	MG	A	D13 D115 E116	D16 D118 E119
BS04	CA	A	D13 M14 D115	D16 M17 D118
BS05	MG	A	D13 M14 D115	D16 M17 D118
BS06	STP	A	D13 M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231	D16 M17 D18 C19 F20 F21 I51 Y55 R58 R64 D118 K227

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding

Biological Process

• GO:0006281 DNA repair

External links

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