PDB entry 2dy4

View 2dy4 on RCSB PDB site
Description: Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
Class: transferase/DNA
Keywords: DNA polymerase, DNA lesion, thymine glycol, oxidative thymine lesion, TRANSFERASE/DNA COMPLEX
Deposited on 2006-09-06, released 2007-01-09
The last revision prior to the SCOPe 2.01 freeze date was dated 2010-01-12, with a file datestamp of 2010-01-08.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: 0.229
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.01: d2dy4a1, d2dy4a2
  • Chain 'B':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.01: d2dy4b1, d2dy4b2
  • Chain 'C':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.01: d2dy4c1, d2dy4c2
  • Chain 'D':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-End)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.01: d2dy4d1, d2dy4d2
  • Chain 'E':
    Compound: 5'-d(*cp*gp*(ctg)p*gp*gp*ap*ap*tp*gp*a*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'F':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*t*cp*ap*tp*tp*cp*cp*a)-3'
  • Chain 'G':
    Compound: 5'-d(*cp*gp*(ctg)p*gp*gp*ap*ap*tp*gp*a*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'H':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*t*cp*ap*tp*tp*cp*cp*a)-3'
  • Chain 'I':
    Compound: 5'-d(*cp*gp*(ctg)p*gp*gp*ap*ap*tp*gp*a*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'J':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*t*cp*ap*tp*tp*cp*cp*a)-3'
  • Chain 'K':
    Compound: 5'-d(*cp*gp*(ctg)p*gp*gp*ap*ap*tp*gp*a*cp*ap*gp*cp*cp*gp*cp*g)-3'
  • Chain 'L':
    Compound: 5'-d(*gp*cp*gp*gp*cp*tp*gp*t*cp*ap*tp*tp*cp*cp*a)-3'
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2dy4A (A:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    fdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy4A (A:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    fd
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2dy4B (B:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    fdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy4B (B:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikdvdyrfdfsdeikekikklsakslnemlfraqrtevagmt
    aqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylnevcgtege
    afvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgfremceym
    nnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklkimgletqk
    sstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssanniakydvg
    gfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkciawpsgtei
    tdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfd
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2dy4C (C:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    fdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy4C (C:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2dy4D (D:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
    mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
    vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
    paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
    aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
    svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
    fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
    fdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >2dy4D (D:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvieiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
    pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
    iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
    etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
    ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
    tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
    vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
    remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
    mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
    iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
    wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkasl
    

  • 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.