Structure of PDB 5db9 Chain A

Receptor sequence
>5db9A (length=327) Species: 9606 (Homo sapiens) [Search protein sequence]
PQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSG
AEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGI
GPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEML
QMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESQP
KLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIR
LIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAG
EPLPVDSEKDIFDYIQWKYREPKDRSE
3D structure
PDB5db9 N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.
ChainA
Resolution2.45 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D190 D192 D256
Catalytic site (residue number reindexed from 1) D184 D186 D248
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
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 H34 S229 K230 G231 T233 K234 Y271 Y296 H28 S221 K222 G223 T225 K226 Y263 Y288
BS02 dna A S104 G105 I106 G107 P108 S109 A110 R254 S98 G99 I100 G101 P102 S103 A104 R246
BS03 dna A K35 Y39 G64 V65 G66 K68 I69 K29 Y33 G58 V59 G60 K62 I63
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0016779 nucleotidyltransferase activity
GO:0016829 lyase activity
GO:0019899 enzyme binding
GO:0034061 DNA polymerase activity
GO:0046872 metal ion binding
GO:0051575 5'-deoxyribose-5-phosphate lyase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0001701 in utero embryonic development
GO:0006259 DNA metabolic process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006290 pyrimidine dimer repair
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006915 apoptotic process
GO:0006954 inflammatory response
GO:0006974 DNA damage response
GO:0007435 salivary gland morphogenesis
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332 response to gamma radiation
GO:0016445 somatic diversification of immunoglobulins
GO:0016446 somatic hypermutation of immunoglobulin genes
GO:0045471 response to ethanol
GO:0048535 lymph node development
GO:0048536 spleen development
GO:0048872 homeostasis of number of cells
GO:0051402 neuron apoptotic process
GO:0055093 response to hyperoxia
GO:0071707 immunoglobulin heavy chain V-D-J recombination
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005874 microtubule
GO:0005876 spindle microtubule
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5db9, PDBe:5db9, PDBj:5db9
PDBsum5db9
PubMed26517568
UniProtP06746|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

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