PDB entry 3l8b

View 3l8b on RCSB PDB site
Description: Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin
Class: transferase/DNA
Keywords: DNA polymerase RB69 gp43, protein-DNA complex, oxidative DNA lesion, guanidinohydantoin, DNA replication, DNA-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase, transferase-DNA complex
Deposited on 2009-12-30, released 2010-03-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2010-04-07, with a file datestamp of 2010-04-02.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: 0.219
AEROSPACI score: 0.39 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43, gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-902)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.07: d3l8ba1, d3l8ba2
  • Chain 'B':
    Compound: DNA polymerase
    Species: Enterobacteria phage RB69 [TaxId:12353]
    Gene: 43, gp43
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q38087 (0-902)
      • engineered (221)
      • engineered (326)
    Domains in SCOPe 2.07: d3l8bb1, d3l8bb2
  • Chain 'C':
    Compound: DNA (5'-d(*ap*c*tp*(g35)p*tp*tp*ap*ap*gp*cp*ap*gp*tp*cp*cp*gp*cp*g)-3')
  • Chain 'D':
    Compound: DNA (5'-d(*gp*cp*gp*gp*ap*cp*tp*gp*cp*tp*tp*ap*a)-3')
  • Chain 'E':
    Compound: DNA (5'-d(*ap*c*tp*(g35)p*tp*tp*ap*ap*gp*cp*ap*gp*tp*cp*cp*gp*cp*g)-3')
  • Chain 'F':
    Compound: DNA (5'-d(*gp*cp*gp*gp*ap*cp*tp*gp*cp*tp*tp*ap*a)-3')
  • Heterogens: SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3l8bA (A:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
fdfhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3l8bA (A:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvieiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3l8bB (B:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
qrkehkgymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslne
mlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierk
vneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarerme
paidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtry
aepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisia
svssanniakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnp
fgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdm
fdfhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >3l8bB (B:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvreiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnisp
etiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkg
ymlaaqrngeiikealhnpnlsvdepldvdyrfdfsdeikekikklsakslnemlfraqr
tevagmtaqinrkllinslygalgnvwfryydlrnataittfgqmalqwierkvneylne
vcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgf
remceymnnkqhlmfmdreaiagpplgskgiggfwtgkkryalnvwdmegtryaepklki
mgletqksstpkavqkalkecirrmlqegeeslqeyfkefekefrqlnyisiasvssann
iakydvggfpgpkcpfhirgiltynraikgnidapqvvegekvyvlplregnpfgdkcia
wpsgteitdlikddvlhwmdytvllektfikplegftsaakldyekkaslfdmfdf

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.