Structure of PDB 5j2a Chain A
Receptor sequence
>5j2aA (length=326) Species:
9606
(Homo sapiens) [
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TLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEA
KKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPS
AARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQ
DIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPK
LLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRL
IPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGE
PLPVDSEKDIFDYIQWKYREPKDRSE
3D structure
PDB
5j2a
Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism.
Chain
A
Resolution
2.5 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)
D181 D183 D247
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 K234 R258 K280 R283 I293 N294 E295 Y296
H25 S220 K221 G222 K225 R249 K271 R274 I284 N285 E286 Y287
BS02
dna
A
G105 G107 P108 S109 A110
G96 G98 P99 S100 A101
BS03
dna
A
K35 A38 Y39 P63 G64 G66 K68 I69
K26 A29 Y30 P54 G55 G57 K59 I60
BS04
DUP
A
G179 S180 R183 D190 D192 Y271 G274 D276 N279
G170 S171 R174 D181 D183 Y262 G265 D267 N270
BS05
MG
A
D190 D192
D181 D183
BS06
MG
A
D190 D192 D256
D181 D183 D247
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
View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB
RCSB:5j2a
,
PDBe:5j2a
,
PDBj:5j2a
PDBsum
5j2a
PubMed
27642161
UniProt
P06746
|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)
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