PDB entry 2p5g

View 2p5g on RCSB PDB site
Description: Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template
Class: transferase/DNA
Keywords: DNA POLYMERASE, ABASIC SITE, DNA LESION, dAMP, transferase-DNA COMPLEX
Deposited on 2007-03-15, released 2007-10-23
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-10-18, with a file datestamp of 2017-10-13.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: N/A
AEROSPACI score: 0.15 (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 (0-902)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.07: d2p5ga1, d2p5ga2
  • Chain 'B':
    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 (326)
    Domains in SCOPe 2.07: d2p5gb1, d2p5gb2
  • 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 (326)
    Domains in SCOPe 2.07: d2p5gc1, d2p5gc2
  • Chain 'D':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.07: d2p5gd1, d2p5gd2
  • Chain 'E':
    Compound: Template DNA
  • Chain 'F':
    Compound: Primer DNA
  • Chain 'G':
    Compound: Template DNA
  • Chain 'H':
    Compound: Primer DNA
  • Chain 'I':
    Compound: Template DNA
  • Chain 'J':
    Compound: Primer DNA
  • Chain 'K':
    Compound: Template DNA
  • Chain 'L':
    Compound: Primer DNA
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2p5gA (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)
    >2p5gA (A:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealhyrfdfsdeikekikklsakslnemlfraqrtevagm
    taqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylnevcgteg
    eafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgfremcey
    mnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklkimgletq
    ksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssanniakydv
    ggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkciawpsgte
    itdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2p5gB (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)
    >2p5gB (B:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqw
    ierkvneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfar
    ermepaidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdme
    gtryaepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlny
    isidytvllektfikplegftsaakldyekkaslfd
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2p5gC (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)
    >2p5gC (C:)
    mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
    lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
    dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
    eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
    rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
    gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
    piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
    rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
    qrkehkgymlaaqrngeiikealdvdyrfddeikekikklsakslnemlfraqrtevagm
    taqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylnevcgteg
    eafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgfremcey
    mnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklkimgletq
    ksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssanniakydv
    ggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkciawpsgte
    itdlikddvlhwmdytvllektfikplegftsaakldyekkaslf
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2p5gD (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)
    >2p5gD (D:)
    kefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrkl
    fanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtspd
    gfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaggdevpseiidki
    iympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestakrlsphr
    ktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkyd
    gpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwd
    aiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnis
    petiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehk
    gymlaaqrngeiikeapldvdyrfddeikekikklsakslnemlfraqrtevagmtaqin
    rkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylnevcgtegeafvl
    ygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgfremceymnnkq
    hlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklkimgletqksstp
    kavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssanniakydvggfpg
    pkcpfhirgiltynraipqvvegekvyvlplregnpfgdkciawpsgteitdlikddvlh
    wmdytvllektfikplegftsaakldyekkaslfd
    

  • 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.