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2P5G
Biol. Unit 2
Info
Asym.Unit (599 KB)
Biol.Unit 1 (165 KB)
Biol.Unit 2 (141 KB)
Biol.Unit 3 (166 KB)
Biol.Unit 4 (139 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RB69 GP43 IN COMPLEX WITH DNA WITH DAMP OPPOSITE AN ABASIC SITE ANALOG IN A 21MER TEMPLATE
Authors
:
K. E. Zahn, H. Belrhali, S. S. Wallace, S. Doublie
Date
:
15 Mar 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (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, Damp, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. E. Zahn, H. Belrhali, S. S. Wallace, S. Doublie
Caught Bending The A-Rule: Crystal Structures Of Translesion Dna Synthesis With A Non-Natural Nucleotide.
Biochemistry V. 46 10551 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 22)
Info
All Hetero Components
1a: 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSP... (3DRa)
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)
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:
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Label:
No.
Name
Count
Type
Full Name
1
3DR
-1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
MSE
22
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(0, 0)
Info
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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 (B:619-627)
;
View:
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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
-
B: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_d2p5ga1 (A:1-375)
1b: SCOP_d2p5gb1 (B:1-375)
1c: SCOP_d2p5gc1 (C:1-375)
1d: SCOP_d2p5gd1 (D:2-375)
2a: SCOP_d2p5ga2 (A:376-903)
2b: SCOP_d2p5gb2 (B:376-899)
2c: SCOP_d2p5gc2 (C:376-898)
2d: SCOP_d2p5gd2 (D:376-899)
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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
d2p5ga1
A:1-375
1b
d2p5gb1
B:1-375
1c
d2p5gc1
C:1-375
1d
d2p5gd1
D:2-375
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
d2p5ga2
A:376-903
2b
d2p5gb2
B:376-899
2c
d2p5gc2
C:376-898
2d
d2p5gd2
D:376-899
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2p5gD02 (D:107-339)
1b: CATH_2p5gA02 (A:107-339)
1c: CATH_2p5gB02 (B:109-341)
1d: CATH_2p5gC02 (C:107-339)
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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)
Enterobacteria phage rb69. Organism_taxid: 12353.
(8)
1a
2p5gD02
D:107-339
1b
2p5gA02
A:107-339
1c
2p5gB02
B:109-341
1d
2p5gC02
C:107-339
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_DNA_pol_B_2p5gD01 (D:362-856)
1b: PFAM_DNA_pol_B_2p5gD02 (D:362-856)
1c: PFAM_DNA_pol_B_2p5gD03 (D:362-856)
1d: PFAM_DNA_pol_B_2p5gD04 (D:362-856)
2a: PFAM_DNA_pol_B_exo1_2p5gD05 (D:28-293)
2b: PFAM_DNA_pol_B_exo1_2p5gD06 (D:28-293)
2c: PFAM_DNA_pol_B_exo1_2p5gD07 (D:28-293)
2d: PFAM_DNA_pol_B_exo1_2p5gD08 (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-2p5gD01
D:362-856
1b
DNA_pol_B-2p5gD02
D:362-856
1c
DNA_pol_B-2p5gD03
D:362-856
1d
DNA_pol_B-2p5gD04
D:362-856
Clan
:
RNase_H
(288)
Family
:
DNA_pol_B_exo1
(38)
Enterobacteria phage RB69 (Bacteriophage RB69)
(20)
2a
DNA_pol_B_exo1-2p5gD05
D:28-293
2b
DNA_pol_B_exo1-2p5gD06
D:28-293
2c
DNA_pol_B_exo1-2p5gD07
D:28-293
2d
DNA_pol_B_exo1-2p5gD08
D:28-293
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