Structure of PDB 5tyd Chain A

Receptor sequence

>5tydA (length=326) Species: 9606 (Homo sapiens)

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVL
KALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQT
MKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDL
STPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLIT
HPKEGQEAGLLPRVMCRLQDQGLILYHQFERSFCIFRLPQPGSWKAVRVD
LVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKT
FFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 5tyd Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
• Chain: A
• Resolution: 1.899 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D194 D196 D250
• 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	L177 F385 E386 R387 R442 R445 R446 R449 K450 L456 N457 H459	L41 F229 E230 R231 R274 R277 R278 R281 K282 L288 N289 H291
BS02	dna	A	G245 V246 G247 T250 D330 D332 F389 R416 D418 G433 W434 G436 K438	G109 V110 G111 T114 D194 D196 F233 R248 D250 G265 W266 G268 K270
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G38 R39 T42 F43 H68 G70 H72 S73
BS04	MG	A	D330 D332 D418	D194 D196 D250
BS05	MG	A	D330 D332	D194 D196
BS06	TTP	A	G319 G320 R323 H329 D330 D332 G433 G436 K438	G183 G184 R187 H193 D194 D196 G265 G268 K270

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5tyd, PDBe:5tyd, PDBj:5tyd
• PDBsum: 5tyd
• PubMed: 28811466
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)