Structure of PDB 3k5n Chain A

Receptor sequence

>3k5nA (length=759) Species: 562 (Escherichia coli)

MAQAGFILTRHWRDTPQGTEVSFWLATDNGPLQVTLAPQESVAFIPADQV
PRAQHILQGEQGFRLTPLALKDFHRQPVYGLYCRAHRQLMNYEKRLREGG
VTVYEADVRPPERYLMERFITSPVWVEGDMHNGTIVNARLKPHPDYRPPL
KWVSIDIETTRHGELYCIGLEGCGQRIVYMLGPENGDASSLDFELEYVAS
RPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQKHAERYRLPLRLGRDN
SELEWFFAQAKGRLIIDGIEALKSAFWNFSSFSLETVAQELLGEGWDRMD
EIDRRFAEDKPALATYNLKNCELVTQIFHKTEIMPFLLERATVNGLPVDR
HGGSVAAFGHLYFPRMHRAGYVAPNLGEVPPHASPGGYVMDSRPGLYDSV
LVLDYKSLYPSIIRTFLIDPVGLVEGMAQPDPEHSTEGFLDAWFSREKHC
LPEIVTNIWHGRDEAKRQGNKPLSQALKIIMNAFYGVLGTTACRFFDPRL
ASSITMRGHQIMRQTKALIEAQGYDVIYGDTDSTFVWLKGAHSEEEAAKI
GRALVQHVNAWWAETLQKQRLTSALELEYETHFCRFLMPTKRYAGLIQEG
DKQRMVFKGLETVRTDWTPLAQQFQQELYLRIFRNEPYQEYVRETIDKLM
AGELDARLVYRKRLRRPLSEYQRNVPPHVRAARLADEENQKRGRPLQYQN
RGTIKYVWTTNGPEPLDYQRSPLDYEHYLTRQLQPVAEGILPFIEDNFAT
LMTGQLGLF

3D structure

• PDB: 3k5n Structural insight into translesion synthesis by DNA Pol II.
• Chain: A
• Resolution: 3.15 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	N698 V699 P701 R755	N674 V675 P677 R731
BS02	dna	A	V637 R638 T639 K686 R687 R689 R690 Y695 R697	V613 R614 T615 K662 R663 R665 R666 Y671 R673

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008296 3'-5'-DNA exonuclease activity

Biological Process

• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0009432 SOS response
• GO:0045004 DNA replication proofreading
• GO:0071897 DNA biosynthetic process

External links

• PDB: RCSB:3k5n, PDBe:3k5n, PDBj:3k5n
• PDBsum: 3k5n
• PubMed: 20064374
• UniProt: P21189|DPO2_ECOLI DNA polymerase II (Gene Name=polB)