Structure of PDB 7m87 Chain A

Receptor sequence

>7m87A (length=429) Species: 9606 (Homo sapiens)

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGPVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAA
IERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIR
KIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCR
GIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLT
KDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVI
KNCNTSGIQTEWSPPLTMLFLCATKFSAS

3D structure

• PDB: 7m87 Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
• Chain: A
• Resolution: 1.85 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 L89 R93 K293 R313 P316 K317 T318 G320 S322 K323 N324 P326 G327 R351	Q41 Y42 W45 R64 S65 K89 L92 R96 K290 R310 P313 K314 T315 G317 S319 K320 N321 P323 G324 R348
BS02	dna	A	F17 F18 I48 R61 D115 E116 K224 S257 G259 G260 K261 L262 R377 L381 R382 R383	F20 F21 I51 R64 D118 E119 K221 S254 G256 G257 K258 L259 R374 L378 R379 R380
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	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 K228

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:7m87, PDBe:7m87, PDBj:7m87
• PDBsum: 7m87
• PubMed: 34088846
• UniProt: Q9Y253|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)