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1YFJ
Biol. Unit 5
Info
Asym.Unit (314 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (57 KB)
Biol.Unit 5 (55 KB)
Biol.Unit 6 (33 KB)
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(1)
Title
:
T4DAM IN COMPLEX WITH ADOHCY AND 15-MER OLIGONUCLEOTIDE SHOWING SEMI-SPECIFIC AND SPECIFIC CONTACT
Authors
:
J. R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng
Date
:
02 Jan 05 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.69
Chains
:
Asym. Unit : A,B,C,D,E,F,0,1,2,3,4,5,6,7,8,9
Biol. Unit 1: A,1,2 (1x)
Biol. Unit 2: B,7,8 (1x)
Biol. Unit 3: C,3,4 (1x)
Biol. Unit 4: D,5,6 (1x)
Biol. Unit 5: E,0,9 (1x)
Biol. Unit 6: F (1x)
Keywords
:
T4Dam, Methyltransferase, Dna, Protein-Dna Complex, Transferase/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Horton, K. Liebert, S. Hattman, A. Jeltsch, X. Cheng
Transition From Nonspecific To Specific Dna Interactions Along The Substrate-Recognition Pathway Of Dam Methyltransferase.
Cell(Cambridge, Mass. ) V. 121 349 2005
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
3b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
3c: S-ADENOSYL-L-HOMOCYSTEINE (SAHc)
3d: S-ADENOSYL-L-HOMOCYSTEINE (SAHd)
3e: S-ADENOSYL-L-HOMOCYSTEINE (SAHe)
3f: S-ADENOSYL-L-HOMOCYSTEINE (SAHf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
SAH
1
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
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Sites
(1, 1)
Info
All Sites
1: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
BC1
SOFTWARE
TYR E:7 , ASN E:10 , LYS E:11 , LEU E:31 , PHE E:32 , CYS E:33 , GLY E:34 , GLY E:35 , SER E:37 , VAL E:38 , ASP E:50 , ILE E:51 , GLN E:52 , HIS E:156 , PHE E:157 , ASP E:171 , TYR E:181 , PHE E:184 , HOH E:408 , HOH E:416
BINDING SITE FOR RESIDUE SAH E 405
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: N6_MTASE (E:168-174)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
N6_MTASE
PS00092
N-6 Adenine-specific DNA methylases signature.
DMA_BPT4
168-174
1
-
-
-
-
E:168-174
-
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1yfja1 (A:1-259)
1b: SCOP_d1yfjb_ (B:)
1c: SCOP_d1yfjc_ (C:)
1d: SCOP_d1yfjd_ (D:)
1e: SCOP_d1yfje_ (E:)
1f: SCOP_d1yfjf_ (F:)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
N6 adenine-specific DNA methylase, DAM
(13)
Protein domain
:
DNA methylase T4DAM
(7)
Bacteriophage T4 [TaxId: 10665]
(5)
1a
d1yfja1
A:1-259
1b
d1yfjb_
B:
1c
d1yfjc_
C:
1d
d1yfjd_
D:
1e
d1yfje_
E:
1f
d1yfjf_
F:
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1yfjA01 (A:1-51,A:147-259)
1b: CATH_1yfjB01 (B:1-51,B:147-259)
1c: CATH_1yfjC01 (C:1-51,C:147-259)
1d: CATH_1yfjD01 (D:1-51,D:147-259)
1e: CATH_1yfjE01 (E:1-51,E:147-259)
1f: CATH_1yfjF01 (F:1-51,F:147-259)
2a: CATH_1yfjA02 (A:52-146)
2b: CATH_1yfjB02 (B:52-146)
2c: CATH_1yfjC02 (C:52-146)
2d: CATH_1yfjD02 (D:52-146)
2e: CATH_1yfjE02 (E:52-146)
2f: CATH_1yfjF02 (F:52-146)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Vaccinia Virus protein VP39
(378)
[unclassified]
(23)
1a
1yfjA01
A:1-51,A:147-259
1b
1yfjB01
B:1-51,B:147-259
1c
1yfjC01
C:1-51,C:147-259
1d
1yfjD01
D:1-51,D:147-259
1e
1yfjE01
E:1-51,E:147-259
1f
1yfjF01
F:1-51,F:147-259
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Adenine-specific Methyltransferase; domain 2
(6)
Homologous Superfamily
:
Adenine-specific Methyltransferase, Domain 2
(6)
[unclassified]
(4)
2a
1yfjA02
A:52-146
2b
1yfjB02
B:52-146
2c
1yfjC02
C:52-146
2d
1yfjD02
D:52-146
2e
1yfjE02
E:52-146
2f
1yfjF02
F:52-146
[
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_MethyltransfD12_1yfjF01 (F:7-235)
1b: PFAM_MethyltransfD12_1yfjF02 (F:7-235)
1c: PFAM_MethyltransfD12_1yfjF03 (F:7-235)
1d: PFAM_MethyltransfD12_1yfjF04 (F:7-235)
1e: PFAM_MethyltransfD12_1yfjF05 (F:7-235)
1f: PFAM_MethyltransfD12_1yfjF06 (F:7-235)
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(
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)
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
MethyltransfD12
(6)
Enterobacteria phage T4 (Bacteriophage T4)
(5)
1a
MethyltransfD12-1yfjF01
F:7-235
1b
MethyltransfD12-1yfjF02
F:7-235
1c
MethyltransfD12-1yfjF03
F:7-235
1d
MethyltransfD12-1yfjF04
F:7-235
1e
MethyltransfD12-1yfjF05
F:7-235
1f
MethyltransfD12-1yfjF06
F:7-235
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Asym.Unit (314 KB)
Header - Asym.Unit
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Biol.Unit 3 (61 KB)
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Biol.Unit 4 (57 KB)
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Biol.Unit 5 (55 KB)
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