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5J2K

Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus

Functional Information from GO Data
ChainGOidnamespacecontents
A0001701biological_processin utero embryonic development
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0003887molecular_functionDNA-directed DNA polymerase activity
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005874cellular_componentmicrotubule
A0005876cellular_componentspindle microtubule
A0006259biological_processDNA metabolic process
A0006260biological_processDNA replication
A0006261biological_processDNA-templated DNA replication
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006287biological_processbase-excision repair, gap-filling
A0006290biological_processpyrimidine dimer repair
A0006297biological_processnucleotide-excision repair, DNA gap filling
A0006303biological_processdouble-strand break repair via nonhomologous end joining
A0006915biological_processapoptotic process
A0006954biological_processinflammatory response
A0006974biological_processDNA damage response
A0007435biological_processsalivary gland morphogenesis
A0008017molecular_functionmicrotubule binding
A0008630biological_processintrinsic apoptotic signaling pathway in response to DNA damage
A0009059biological_processmacromolecule biosynthetic process
A0010332biological_processresponse to gamma radiation
A0016445biological_processsomatic diversification of immunoglobulins
A0016446biological_processsomatic hypermutation of immunoglobulin genes
A0016740molecular_functiontransferase activity
A0016779molecular_functionnucleotidyltransferase activity
A0016829molecular_functionlyase activity
A0019899molecular_functionenzyme binding
A0032991cellular_componentprotein-containing complex
A0034061molecular_functionDNA polymerase activity
A0045471biological_processresponse to ethanol
A0046872molecular_functionmetal ion binding
A0048535biological_processlymph node development
A0048536biological_processspleen development
A0048872biological_processhomeostasis of number of cells
A0051402biological_processneuron apoptotic process
A0051575molecular_function5'-deoxyribose-5-phosphate lyase activity
A0055093biological_processresponse to hyperoxia
A0071707biological_processimmunoglobulin heavy chain V-D-J recombination
A0071897biological_processDNA biosynthetic process
A0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
Functional Information from PDB Data
site_idAC1
Number of Residues23
Detailsbinding site for residue DUP A 401
ChainResidue
AGLY179
ATHR273
AGLY274
AASP276
AASN279
AMG402
AMG403
AHOH513
AHOH529
AHOH531
AHOH577
ASER180
AHOH664
PDT10
PHOH102
TDA6
AARG183
ASER188
AGLY189
AASP190
AASP192
ATYR271
APHE272

site_idAC2
Number of Residues5
Detailsbinding site for residue MG A 402
ChainResidue
AASP190
AASP192
ADUP401
AMG403
AHOH529

site_idAC3
Number of Residues7
Detailsbinding site for residue MG A 403
ChainResidue
AASP190
AASP192
AASP256
ADUP401
AMG402
AHOH531
PHOH102

site_idAC4
Number of Residues6
Detailsbinding site for residue NA A 404
ChainResidue
ATHR101
AVAL103
AILE106
AHOH769
PDG9
PHOH105

site_idAC5
Number of Residues6
Detailsbinding site for residue NA A 405
ChainResidue
ALYS60
ALEU62
AVAL65
AHOH592
DDC3
DHOH107

site_idAC6
Number of Residues4
Detailsbinding site for residue CL A 406
ChainResidue
AGLN264
ATYR266
ACYS267
AHOH613

site_idAC7
Number of Residues2
Detailsbinding site for residue CL A 407
ChainResidue
AALA32
AHIS34

site_idAC8
Number of Residues2
Detailsbinding site for residue CL A 408
ChainResidue
ALEU82
AARG89

site_idAC9
Number of Residues3
Detailsbinding site for residue CL A 409
ChainResidue
AASN294
ATHR297
AARG299

Functional Information from PROSITE/UniProt
site_idPS00522
Number of Residues20
DetailsDNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP
ChainResidueDetails
AGLY179-PRO198

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269|PubMed:9572863
ChainResidueDetails
ALYS72

site_idSWS_FT_FI2
Number of Residues6
DetailsBINDING: BINDING => ECO:0000269|PubMed:12517346, ECO:0000269|PubMed:8841120, ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPX, ECO:0007744|PDB:1BPZ, ECO:0007744|PDB:1MQ3, ECO:0007744|PDB:1ZQO, ECO:0007744|PDB:1ZQQ
ChainResidueDetails
ALYS60
ALEU62
AVAL65
ATHR101
AVAL103
AILE106

site_idSWS_FT_FI3
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICW, ECO:0007744|PDB:8ICX, ECO:0007744|PDB:8ICY
ChainResidueDetails
AARG149
ASER180
AGLY189

site_idSWS_FT_FI4
Number of Residues1
DetailsBINDING: BINDING => ECO:0000269|PubMed:8841119, ECO:0007744|PDB:8ICX
ChainResidueDetails
AARG183

site_idSWS_FT_FI5
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:9287163, ECO:0007744|PDB:1BPY
ChainResidueDetails
AASP190
AASP192
AASP256

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q8K409
ChainResidueDetails
ALYS72

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269|PubMed:16600869
ChainResidueDetails
AARG83
AARG152

site_idSWS_FT_FI8
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19713937, ECO:0000269|PubMed:21362556
ChainResidueDetails
ALYS41
ALYS61
ALYS81

217705

PDB entries from 2024-03-27

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