Structure of PDB 4yd1 Chain A

Receptor sequence

>4yd1A (length=334) Species: 9606 (Homo sapiens)

MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCHMDAFERSFCIFRLPQPG
SWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHG
LFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 4yd1 Creative template-dependent synthesis by human polymerase mu.
• Chain: A
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D193 D195 D258
• 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 Q366 H367 D383 A384 R442 R445 R449 K450 L456 N457	L40 Q229 H230 D235 A236 R282 R285 R289 K290 L296 N297
BS02	dna	A	G245 V246 G247 T250 Q366 R387 F389 D418 W434	G108 V109 G110 T113 Q229 R239 F241 D258 W274
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G37 R38 T41 F42 H67 G69 H71 S72
BS04	MG	A	D330 D332 D418	D193 D195 D258
BS05	MG	A	D330 D332	D193 D195
BS06	DUP	A	G319 G320 R323 G328 H329 D330 D332 G433 W434 G436 K438	G182 G183 R186 G191 H192 D193 D195 G273 W274 G276 K278

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:4yd1, PDBe:4yd1, PDBj:4yd1
• PDBsum: 4yd1
• PubMed: 26240373
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)