PDB entry 1rv2

View 1rv2 on RCSB PDB site
Description: Crystal structure of RB69 gp43 in complex with DNA containing an abasic site analog
Class: transferase/DNA
Keywords: DNA polymerase, abasic site, DNA lesion, exonuclease switch
Deposited on 2003-12-12, released 2004-04-20
The last revision prior to the SCOPe 2.07 freeze date was dated 2007-04-03, with a file datestamp of 2007-04-25.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.246
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

• Chain 'A':
  Compound: DNA polymerase
  Species: Bacteriophage RB69
  Gene: 43
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q38087 (0-End)
    • modified residue (0)
    • modified residue (64)
    • modified residue (74)
    • modified residue (84)
    • modified residue (188)
    • modified residue (198)
    • engineered (221)
    • modified residue (255)
    • engineered (326)
    • modified residue (346)
    • modified residue (407)
    • modified residue (460-461)
    • modified residue (488)
    • modified residue (540)
    • modified residue (552)
    • modified residue (591)
    • modified residue (658)
    • modified residue (669)
    • modified residue (673)
    • modified residue (680)
    • modified residue (682)
    • modified residue (714)
    • modified residue (727)
    • modified residue (751)
    • modified residue (865)
    • modified residue (899)
• Chain 'B':
  Compound: DNA polymerase
  Species: Bacteriophage RB69
  Gene: 43
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q38087 (0-End)
    • modified residue (0)
    • modified residue (64)
    • modified residue (74)
    • modified residue (84)
    • modified residue (188)
    • modified residue (198)
    • engineered (221)
    • modified residue (255)
    • engineered (326)
    • modified residue (346)
    • modified residue (407)
    • modified residue (460-461)
    • modified residue (488)
    • modified residue (540)
    • modified residue (552)
    • modified residue (591)
    • modified residue (658)
    • modified residue (669)
    • modified residue (673)
    • modified residue (680)
    • modified residue (682)
    • modified residue (714)
    • modified residue (727)
    • modified residue (751)
    • modified residue (865)
    • modified residue (899)
• Chain 'C':
  Compound: DNA polymerase
  Species: Bacteriophage RB69
  Gene: 43
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q38087 (0-End)
    • modified residue (0)
    • modified residue (64)
    • modified residue (74)
    • modified residue (84)
    • modified residue (188)
    • modified residue (198)
    • engineered (221)
    • modified residue (255)
    • engineered (326)
    • modified residue (346)
    • modified residue (407)
    • modified residue (460-461)
    • modified residue (488)
    • modified residue (540)
    • modified residue (552)
    • modified residue (591)
    • modified residue (658)
    • modified residue (669)
    • modified residue (673)
    • modified residue (680)
    • modified residue (682)
    • modified residue (714)
    • modified residue (727)
    • modified residue (751)
    • modified residue (865)
• Chain 'D':
  Compound: DNA polymerase
  Species: Bacteriophage RB69
  Gene: 43
  Database cross-references and differences (RAF-indexed):
  • Uniprot Q38087 (0-End)
    • modified residue (0)
    • modified residue (64)
    • modified residue (74)
    • modified residue (84)
    • modified residue (188)
    • modified residue (198)
    • engineered (221)
    • engineered (326)
    • modified residue (346)
    • modified residue (407)
    • modified residue (460-461)
    • modified residue (488)
    • modified residue (540)
    • modified residue (552)
    • modified residue (591)
    • modified residue (658)
    • modified residue (669)
    • modified residue (673)
    • modified residue (680)
    • modified residue (682)
    • modified residue (714)
    • modified residue (727)
    • modified residue (751)
    • modified residue (865)
  Domains in SCOPe 2.07: d1rv2d3, d1rv2d4
• 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':
  No sequence available.
  
  
• Chain 'B':
  No sequence available.
  
  
• Chain 'C':
  No sequence available.
  
  
• Chain 'D':
  Sequence, based on SEQRES records: (download)
  

  >1rv2D (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)
  

  >1rv2D (D:)
  mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
  lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
  dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
  eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
  rlsphrktrvkveiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydgp
  isklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwdai
  ifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvnispe
  tiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrkehkgy
  mlaaqrngeiikeaslnemlfraqrtevagmtaqinrkllinslygalgnvwfryydlrn
  ataittfgqmalqwierkvneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfr
  dtnhwvdfldkfarermepaidrgfremceymnnkqhlmfmdreaiagpplgskgiggfw
  tgkkryalnvwdmegtryaepklkimgletqksstpkavqkalkecirrmlqegeeslqe
  yfkefekefrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraipqvvege
  kvyvlplregnpfgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsaak
  ldyekkas
  

  
  
• 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.