Structure of PDB 6ipd Chain A

Receptor sequence

>6ipdA (length=326) Species: 9606 (Homo sapiens)

MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHFERSFCIFRLPQPGSWKAVRVD
LVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKT
FFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 6ipd Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
• Chain: A
• Resolution: 1.7 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D193 D195 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	L40 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	G108 V109 G110 T113 D193 D195 F233 R248 D250 G265 W266 G268 K270
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G37 R38 T41 F42 H67 G69 H71 S72
BS04	MN	A	D330 D332	D193 D195
BS05	MN	A	D330 D332 D418	D193 D195 D250
BS06	OXD	A	G319 G320 R323 D330	G182 G183 R186 D193

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:6ipd, PDBe:6ipd, PDBj:6ipd
• PDBsum: 6ipd
• PubMed: 31067051
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)