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2P5G
Asym. Unit
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
(2, 95)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3DR
1
Mod. Nucleotide
1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2
MSE
94
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER C:360 , PRO C:361 , ILE C:362 , GLY C:568 , ASN C:572 , HOH C:996 , DG I:5 , DC I:7
BINDING SITE FOR RESIDUE 3DR I 6
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_B (A:619-627,B:619-627,C:619-627,D:61...)
;
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
4
A:619-627
B:619-627
C:619-627
D: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.
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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(
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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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Asym.Unit (599 KB)
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Biol.Unit 1 (165 KB)
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Biol.Unit 3 (166 KB)
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