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2P5O
Biol. Unit 1
Info
Asym.Unit (578 KB)
Biol.Unit 1 (164 KB)
Biol.Unit 2 (148 KB)
Biol.Unit 3 (163 KB)
Biol.Unit 4 (115 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RB69 GP43 IN COMPLEX WITH DNA CONTAINING AN ABASIC SITE ANALOG
Authors
:
M. Hogg, S. S. Wallace, S. Doublie
Date
:
15 Mar 07 (Deposition) - 03 Apr 07 (Release) - 10 Sep 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,E,F (1x)
Biol. Unit 2: B,G,H (1x)
Biol. Unit 3: C,I,J (1x)
Biol. Unit 4: D,K,L (1x)
Keywords
:
Dna Polymerase, Abasic Site, Dna Lesion, Exonuclease Switch, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hogg, S. S. Wallace, S. Doublie
Crystallographic Snapshots Of A Replicative Dna Polymerase Encountering An Abasic Site.
Embo J. V. 23 1483 2004
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Hetero Components
(2, 26)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
1b: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRb)
2a: SELENOMETHIONINE (MSEa)
2aa: SELENOMETHIONINE (MSEaa)
2ab: SELENOMETHIONINE (MSEab)
2ac: SELENOMETHIONINE (MSEac)
2ad: SELENOMETHIONINE (MSEad)
2ae: SELENOMETHIONINE (MSEae)
2af: SELENOMETHIONINE (MSEaf)
2ag: SELENOMETHIONINE (MSEag)
2ah: SELENOMETHIONINE (MSEah)
2ai: SELENOMETHIONINE (MSEai)
2aj: SELENOMETHIONINE (MSEaj)
2ak: SELENOMETHIONINE (MSEak)
2al: SELENOMETHIONINE (MSEal)
2am: SELENOMETHIONINE (MSEam)
2an: SELENOMETHIONINE (MSEan)
2ao: SELENOMETHIONINE (MSEao)
2ap: SELENOMETHIONINE (MSEap)
2aq: SELENOMETHIONINE (MSEaq)
2ar: SELENOMETHIONINE (MSEar)
2as: SELENOMETHIONINE (MSEas)
2at: SELENOMETHIONINE (MSEat)
2au: SELENOMETHIONINE (MSEau)
2av: SELENOMETHIONINE (MSEav)
2aw: SELENOMETHIONINE (MSEaw)
2ax: SELENOMETHIONINE (MSEax)
2ay: SELENOMETHIONINE (MSEay)
2az: SELENOMETHIONINE (MSEaz)
2b: SELENOMETHIONINE (MSEb)
2ba: SELENOMETHIONINE (MSEba)
2bb: SELENOMETHIONINE (MSEbb)
2bc: SELENOMETHIONINE (MSEbc)
2bd: SELENOMETHIONINE (MSEbd)
2be: SELENOMETHIONINE (MSEbe)
2bf: SELENOMETHIONINE (MSEbf)
2bg: SELENOMETHIONINE (MSEbg)
2bh: SELENOMETHIONINE (MSEbh)
2bi: SELENOMETHIONINE (MSEbi)
2bj: SELENOMETHIONINE (MSEbj)
2bk: SELENOMETHIONINE (MSEbk)
2bl: SELENOMETHIONINE (MSEbl)
2bm: SELENOMETHIONINE (MSEbm)
2bn: SELENOMETHIONINE (MSEbn)
2bo: SELENOMETHIONINE (MSEbo)
2bp: SELENOMETHIONINE (MSEbp)
2bq: SELENOMETHIONINE (MSEbq)
2br: SELENOMETHIONINE (MSEbr)
2bs: SELENOMETHIONINE (MSEbs)
2bt: SELENOMETHIONINE (MSEbt)
2bu: SELENOMETHIONINE (MSEbu)
2bv: SELENOMETHIONINE (MSEbv)
2bw: SELENOMETHIONINE (MSEbw)
2bx: SELENOMETHIONINE (MSEbx)
2by: SELENOMETHIONINE (MSEby)
2bz: SELENOMETHIONINE (MSEbz)
2c: SELENOMETHIONINE (MSEc)
2ca: SELENOMETHIONINE (MSEca)
2cb: SELENOMETHIONINE (MSEcb)
2cc: SELENOMETHIONINE (MSEcc)
2cd: SELENOMETHIONINE (MSEcd)
2ce: SELENOMETHIONINE (MSEce)
2cf: SELENOMETHIONINE (MSEcf)
2cg: SELENOMETHIONINE (MSEcg)
2ch: SELENOMETHIONINE (MSEch)
2ci: SELENOMETHIONINE (MSEci)
2cj: SELENOMETHIONINE (MSEcj)
2ck: SELENOMETHIONINE (MSEck)
2cl: SELENOMETHIONINE (MSEcl)
2cm: SELENOMETHIONINE (MSEcm)
2cn: SELENOMETHIONINE (MSEcn)
2co: SELENOMETHIONINE (MSEco)
2cp: SELENOMETHIONINE (MSEcp)
2cq: SELENOMETHIONINE (MSEcq)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
2x: SELENOMETHIONINE (MSEx)
2y: SELENOMETHIONINE (MSEy)
2z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
MSE
25
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(0, 0)
Info
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Sorry, no Info available
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:619-627)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_B
PS00116
DNA polymerase family B signature.
DPOL_BPR69
619-627
1
A:619-627
-
-
-
[
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2p5oa1 (A:1-375)
1b: SCOP_d2p5ob1 (B:1-375)
1c: SCOP_d2p5oc1 (C:1-375)
1d: SCOP_d2p5od1 (D:1-375)
2a: SCOP_d2p5oa2 (A:376-902)
2b: SCOP_d2p5ob2 (B:376-901)
2c: SCOP_d2p5oc2 (C:376-898)
2d: SCOP_d2p5od2 (D:376-896)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Ribonuclease H-like
(775)
Family
:
DnaQ-like 3'-5' exonuclease
(253)
Protein domain
:
Exonuclease domain of family B DNA polymerases
(102)
Bacteriophage RB69 [TaxId: 12353]
(92)
1a
d2p5oa1
A:1-375
1b
d2p5ob1
B:1-375
1c
d2p5oc1
C:1-375
1d
d2p5od1
D:1-375
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
DNA polymerase I
(233)
Protein domain
:
Family B DNA polymerase
(100)
Bacteriophage RB69 [TaxId: 12353]
(92)
2a
d2p5oa2
A:376-902
2b
d2p5ob2
B:376-901
2c
d2p5oc2
C:376-898
2d
d2p5od2
D:376-896
[
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]
CATH Domains
(2, 5)
Info
all CATH domains
1a: CATH_2p5oB02 (B:109-341)
1b: CATH_2p5oA02 (A:108-339)
1c: CATH_2p5oC02 (C:108-339)
2a: CATH_2p5oA04 (A:469-572)
2b: CATH_2p5oC04 (C:469-572)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.10, no name defined]
(372)
[unclassified]
(102)
1a
2p5oB02
B:109-341
1b
2p5oA02
A:108-339
1c
2p5oC02
C:108-339
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(10)
[unclassified]
(7)
2a
2p5oA04
A:469-572
2b
2p5oC04
C:469-572
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2p5oD01 (D:362-779)
1b: PFAM_DNA_pol_B_2p5oD02 (D:362-779)
1c: PFAM_DNA_pol_B_2p5oD03 (D:362-779)
1d: PFAM_DNA_pol_B_2p5oD04 (D:362-779)
2a: PFAM_DNA_pol_B_exo1_2p5oD05 (D:28-293)
2b: PFAM_DNA_pol_B_exo1_2p5oD06 (D:28-293)
2c: PFAM_DNA_pol_B_exo1_2p5oD07 (D:28-293)
2d: PFAM_DNA_pol_B_exo1_2p5oD08 (D:28-293)
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(
)
Clan
:
DNA_pol_B-like
(44)
Family
:
DNA_pol_B
(38)
Enterobacteria phage RB69 (Bacteriophage RB69)
(20)
1a
DNA_pol_B-2p5oD01
D:362-779
1b
DNA_pol_B-2p5oD02
D:362-779
1c
DNA_pol_B-2p5oD03
D:362-779
1d
DNA_pol_B-2p5oD04
D:362-779
Clan
:
RNase_H
(288)
Family
:
DNA_pol_B_exo1
(38)
Enterobacteria phage RB69 (Bacteriophage RB69)
(20)
2a
DNA_pol_B_exo1-2p5oD05
D:28-293
2b
DNA_pol_B_exo1-2p5oD06
D:28-293
2c
DNA_pol_B_exo1-2p5oD07
D:28-293
2d
DNA_pol_B_exo1-2p5oD08
D:28-293
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Asym.Unit (578 KB)
Header - Asym.Unit
Biol.Unit 1 (164 KB)
Header - Biol.Unit 1
Biol.Unit 2 (148 KB)
Header - Biol.Unit 2
Biol.Unit 3 (163 KB)
Header - Biol.Unit 3
Biol.Unit 4 (115 KB)
Header - Biol.Unit 4
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