Structure of PDB 5kg6 Chain A

Receptor sequence

>5kg6A (length=431) Species: 9606 (Homo sapiens)

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGPETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMR
AAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMP
IRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAM
CRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEER
LTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFT
VIKNCNTSGIQTEWSPPLTMLFLCATKFSAS

3D structure

• PDB: 5kg6 Capture of a third Mg2+ is essential for catalyzing DNA synthesis.
• Chain: A
• Resolution: 1.55 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 K311 R313 P316 K317 T318 G320 S322 K323 N324 P326	Q41 Y42 W45 R64 S65 W67 K89 R96 K310 R312 P315 K316 T317 G319 S321 K322 N323 P325
BS02	dna	A	F18 R61 S113 D115 E116 S257 G259 G260 K261 L262 R377 R382 C384	F21 R64 S116 D118 E119 S256 G258 G259 K260 L261 R376 R381 C383
BS03	MN	A	D13 D115 E116	D16 D118 E119
BS04	MN	A	D13 M14 D115	D16 M17 D118
BS05	DTP	A	D13 M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231	D16 M17 D18 C19 F20 F21 I51 Y55 R58 R64 D118 K230

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5kg6, PDBe:5kg6, PDBj:5kg6
• PDBsum: 5kg6
• PubMed: 27284197
• UniProt: Q9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)