SCOPe 2.08: Structural Classification of Proteins

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 2.08 freeze date was dated 2017-10-11, with a file datestamp of 2017-10-06.
Experiment type: XRAY
Resolution: 2.65 Å
R-factor: N/A
AEROSPACI score: 0.17 (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 2.08: 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 2.08: 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 2.08: 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 2.08: 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.