Structure of PDB 5kfi Chain A

Receptor sequence

>5kfiA (length=430) Species: 9606 (Homo sapiens)

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGPTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRA
AIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPI
RKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMC
RGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERL
TKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTV
IKNCNTSGIQTEWSPPLTMLFLCATKFSAS

3D structure

• PDB: 5kfi Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
• Chain: A
• Resolution: 1.65 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 K86 R93 K311 P316 K317 T318 G320 S322 K323 N324 P326 G327 R351	Q41 Y42 W45 R64 S65 K89 R96 K309 P314 K315 T316 G318 S320 K321 N322 P324 G325 R349
BS02	dna	A	F18 I48 R61 S113 D115 E116 K224 S257 G259 G260 K261 L262 R377 L381 R382 C384	F21 I51 R64 S116 D118 E119 K222 S255 G257 G258 K259 L260 R375 L379 R380 C382
BS03	MN	A	D13 D115 E116	D16 D118 E119
BS04	CA	A	D13 M14 D115	D16 M17 D118
BS05	MN	A	D13 M14 D115	D16 M17 D118
BS06	DTP	A	D13 D15 C16 F17 F18 Y52 R55 R61 D115 K231	D16 D18 C19 F20 F21 Y55 R58 R64 D118 K229

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding

Biological Process

• GO:0006281 DNA repair

External links

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