SCOPe 2.08: Structural Classification of Proteins

PDB entry 2p5o

View 2p5o 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, transferase-DNA COMPLEX
Deposited on 2007-03-15, released 2007-04-03
The last revision prior to the SCOPe 2.08 freeze date was dated 2014-09-10, with a file datestamp of 2014-09-05.
Experiment type: XRAY
Resolution: 2.8 Å
R-factor: 0.245
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 (1-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)
Domains in SCOPe 2.08: d2p5oa1, d2p5oa2
Chain 'B':
Compound: DNA polymerase
Species: Enterobacteria phage RB69 [TaxId:12353]
Gene: 43
Database cross-references and differences (RAF-indexed):
- Uniprot Q38087 (1-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)
Domains in SCOPe 2.08: d2p5ob1, d2p5ob2
Chain 'C':
Compound: DNA polymerase
Species: Enterobacteria phage RB69 [TaxId:12353]
Gene: 43
Database cross-references and differences (RAF-indexed):
- Uniprot Q38087 (1-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)
Domains in SCOPe 2.08: d2p5oc1, d2p5oc2
Chain 'D':
Compound: DNA polymerase
Species: Enterobacteria phage RB69 [TaxId:12353]
Gene: 43
Database cross-references and differences (RAF-indexed):
- Uniprot Q38087 (1-End)
  - modified residue (0)
  - modified residue (64)
  - modified residue (74)
  - modified residue (84)
  - modified residue (198)
  - engineered (221)
  - engineered (326)
  - modified residue (346)
  - modified residue (407)
  - modified residue (460-461)
  - 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 2.08: d2p5od1, d2p5od2
Chain 'E':
Compound: Template DNA
Species: synthetic, synthetic
Chain 'F':
Compound: Primer DNA
Species: synthetic, synthetic
Chain 'G':
Compound: Template DNA
Species: synthetic, synthetic
Chain 'H':
Compound: Primer DNA
Species: synthetic, synthetic
Chain 'I':
Compound: Template DNA
Species: synthetic, synthetic
Chain 'J':
Compound: Primer DNA
Species: synthetic, synthetic
Chain 'K':
Compound: Template DNA
Species: synthetic, synthetic
Chain 'L':
Compound: Primer DNA
Species: synthetic, synthetic
Heterogens: HOH

PDB Chain Sequences:

Chain 'A':
Sequence, based on SEQRES records: (download)

>2p5oA (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)

>2p5oA (A:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
qrkehkgymlaaqrmlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnatai
ttfgqmalqwierkvneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnh
wvdfldkfarermepaidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkk
ryalnvwdmegtryaepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfke
fekefrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvve
gekvyvlplregnpfgdkciawpsgteitdlikddvlhwmdytvllektfikplegftsa
akldyekkaslfdmfd

Chain 'B':
Sequence, based on SEQRES records: (download)

>2p5oB (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)

>2p5oB (B:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmeiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklk
ydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspikt
wdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsiirqvn
ispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfnqrke
hkgymlaaqrnmlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnataittf
gqmalqwierkvneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtnhwvd
fldkfarermepaidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgkkrya
lnvwdmegtryaepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfkefek
efrqlnyisidvlhwmdytvllektfikplegftsaakldyekkaslfdmf

Chain 'C':
Sequence, based on SEQRES records: (download)

>2p5oC (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)

>2p5oC (C:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslkeqnkvipqgrshpvqpypgafvkepipnrykyvmsfdltslypsii
rqvnispetiagtfkvaplhdyinavaerpsdvyscspngmmyykdrdgvvpteitkvfn
qrkehkgymlaaqrnmlfraqrtevagmtaqinrkllinslygalgnvwfryydlrnata
ittfgqmalqwierkvneylnevcgtegeafvlygdtdsiyvsadkiidkvgeskfrdtn
hwvdfldkfarermepaidrgfremceymnnkqhlmfmdreaiagpplgskgiggfwtgk
kryalnvwdmegtryaepklkimgletqksstpkavqkalkecirrmlqegeeslqeyfk
efekefrqlnyisiasvssanniakydvggfpgpkcpfhirgiltynraikgnidapqvv
egekvyvlplregnpfgdkciawpsgteitdlikddvlhwmdytvllektfikplegfts
aakldyekkaslf

Chain 'D':
Sequence, based on SEQRES records: (download)

>2p5oD (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)

>2p5oD (D:)
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirfdnekellmey
lnfwqqktpviltgwnvesfaipyvynriknifgestakrlsphrktrvkveiitlfgis
vldyidlykkfsftnqpsysldyisefelnvgklkydgpisklresnhqryisyniiavy
rvlqidakrqfinlsldmgyyakiqiqsvfspiktwdaiifnslkeqnkvipqgrshpvq
pypgafvkepipnrykyvmsfdltslypsiirqvnispetiagtfkvaplhdyinavaer
psdvyscspngmmyykdrdgvvpteitkvfnqslnemlfraqrtevagmtaqinrkllin
slygalgnvwfryydlrnataittfgqmalqwierkvneylnevcgtegeafvlygdtds
iyvsadkiidkvgeskfrdtnhwvdfldkfarermepaidrgfremceymnnkqhlmfmd
reaiagpplgskgiggfwtgkkryalnvwdmegtryaepklkimgletqksstpkavqka
lkecirrmlqegeeslqeyfkefekefrqlnyisidvlhwmdytvllektfikplegfts
aakldyekkas

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.