PDB entry 2dtu

View 2dtu on RCSB PDB site
Description: Crystal structure of the beta hairpin loop deletion variant of RB69 gp43 in complex with DNA containing an abasic site analog
Class: transferase/DNA
Keywords: DNA polymerase, abasic site, DNA lesion, beta hairpin deletion, transferase-DNA complex
Deposited on 2006-07-15, released 2006-12-05
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-10-11, with a file datestamp of 2017-10-06.
Experiment type: XRAY
Resolution: 2.37 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-894)
      • engineered (221)
      • engineered (252)
      • engineered (319)
    Domains in SCOPe 2.08: d2dtua1, d2dtua2
  • Chain 'B':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-894)
      • engineered (221)
      • engineered (252)
      • engineered (319)
    Domains in SCOPe 2.08: d2dtub1, d2dtub2
  • Chain 'C':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (252)
      • engineered (319)
    Domains in SCOPe 2.08: d2dtuc1, d2dtuc2
  • Chain 'D':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (252)
      • engineered (319)
    Domains in SCOPe 2.08: d2dtud1, d2dtud2
  • Chain 'E':
    Compound: 5'-d(*cp*gp*(3dr)p*cp*tp*tp*ap*tp*gp*ap*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'F':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*tp*cp*ap*tp*ap*ap*gp*a)-3'
  • Chain 'G':
    Compound: 5'-d(*cp*gp*(3dr)p*cp*tp*tp*ap*tp*gp*ap*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'H':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*tp*cp*ap*tp*ap*ap*gp*a)-3'
  • Chain 'I':
    Compound: 5'-d(*cp*gp*(3dr)p*cp*tp*tp*ap*tp*gp*ap*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'J':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*tp*cp*ap*tp*ap*ap*gp*a)-3'
  • Chain 'K':
    Compound: 5'-d(*cp*gp*(3dr)p*cp*tp*tp*ap*tp*gp*ap*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'L':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*tp*cp*ap*tp*ap*ap*gp*a)-3'
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2dtuA (A:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2dtuB (B:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2dtuC (C:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

    Sequence, based on observed residues (ATOM records): (download) 
    >2dtuC (C:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfd

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2dtuD (D:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

    Sequence, based on observed residues (ATOM records): (download) 
    >2dtuD (D:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvgeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslf

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.