Structure of PDB 6vfa Chain A

Receptor sequence

>6vfaA (length=327) Species: 9606 (Homo sapiens)

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVL
KALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQT
MKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDL
STPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLIT
HPKEGQEAGLLPRVMCRLQDQGLILYHQAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 6vfa DNA Polymerase Mu, 8-oxorGTP:Ct Ground State Ternary Complex, 50 mM Mn2+ (15 min)
• Chain: A
• Resolution: 1.76 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	L177 F385 E386 R387 R442 R445 R449 K450 N457	L41 F230 E231 R232 R275 R278 R282 K283 N290
BS02	dna	A	G245 V246 G247 T250 H329 R416	G109 V110 G111 T114 H193 R249
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G38 R39 T42 F43 H68 G70 H72 S73
BS04	MN	A	D330 D332 D418	D194 D196 D251
BS05	MN	A	D330 D332	D194 D196
BS06	MN	A	E218 H219	E82 H83
BS07	MN	A	E386 H459	E231 H292
BS08	8GT	A	Q242 G320 R323 H329 D330 D332 K438	Q106 G184 R187 H193 D194 D196 K271

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