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Asym. Unit
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Asym.Unit (121 KB)
Biol.Unit 1 (115 KB)
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(1)
Title
:
STRUCTURE OF DCPS BOUND TO M7GPPPG
Authors
:
M. Gu, C. Fabrega, S. W. Liu, H. Liu, M. Kiledjian, C. D. Lima
Date
:
24 Mar 04 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rna Decay, Exosome, Decapping, Hit Protein, Messenger Rna, Mrna, Cap, Rna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Gu, C. Fabrega, S. W. Liu, H. Liu, M. Kiledjian, C. D. Lima
Insights Into The Structure, Mechanism, And Regulation Of Scavenger Mrna Decapping Activity
Mol. Cell V. 14 67 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE... (GTGa)
1b: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE... (GTGb)
2a: YTTRIUM (III) ION (YT3a)
2b: YTTRIUM (III) ION (YT3b)
2c: YTTRIUM (III) ION (YT3c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GTG
2
Ligand/Ion
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
2
YT3
3
Ligand/Ion
YTTRIUM (III) ION
[
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:74 , GLU A:92 , YT3 A:702 , HOH A:955
BINDING SITE FOR RESIDUE YT3 A 701
2
AC2
SOFTWARE
ASP A:74 , ASP A:76 , GLU A:92 , YT3 A:701 , HOH A:943
BINDING SITE FOR RESIDUE YT3 A 702
3
AC3
SOFTWARE
ASP A:76 , HOH A:919 , HOH A:932 , HOH A:935
BINDING SITE FOR RESIDUE YT3 A 703
4
AC4
SOFTWARE
ARG A:54 , ASP A:59 , ILE A:61 , GLU A:85 , LYS A:128 , LYS A:142 , TRP A:175 , GLU A:185 , PRO A:204 , ASP A:205 , LEU A:206 , LYS A:207 , HIS A:268 , PRO A:271 , SER A:272 , TYR A:273 , ASN A:277 , HIS A:279 , PRO A:288 , ARG A:294 , HOH A:704 , HOH A:708 , HOH A:737 , HOH A:738 , HOH A:741 , HOH A:751 , HOH A:771 , HOH A:809 , HOH A:814 , HOH A:838 , HOH A:868 , PHE B:108 , ASN B:110 , TYR B:113
BINDING SITE FOR RESIDUE GTG A 651
5
AC5
SOFTWARE
ARG B:145 , TRP B:175 , GLU B:185 , ARG B:188 , ILE B:203 , PRO B:204 , ASP B:205 , LEU B:206 , LYS B:207 , ILE B:219 , HIS B:268 , PRO B:271 , SER B:272 , TYR B:273 , ASN B:277 , HIS B:279 , ARG B:294 , ARG B:322 , HOH B:695 , HOH B:918 , HOH B:919 , HOH B:940
BINDING SITE FOR RESIDUE GTG B 652
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_027958 (G73E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_027958
G
73
E
DCPS_HUMAN
Polymorphism
11557735
A/B
G
73
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: HIT_1 (A:264-282,B:264-282)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HIT_1
PS00892
HIT domain signature.
DCPS_HUMAN
264-282
2
A:264-282
B:264-282
[
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Exons
(6, 12)
Info
All Exons
Exon 1.1 (A:38-67 | B:40-67)
Exon 1.2 (A:68-126 | B:68-126)
Exon 1.3b (A:126-174 | B:126-174)
Exon 1.4b (A:175-212 | B:175-212)
Exon 1.5 (A:213-249 | B:213-249)
Exon 1.6b (A:250-337 | B:250-336)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3b
4: Boundary 1.3b/1.4b
5: Boundary 1.4b/1.5
6: Boundary 1.5/1.6b
7: Boundary 1.6b/-
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000263579
1
ENSE00001324469
chr11:
126173647-126174176
530
DCPS_HUMAN
1-67
67
2
A:38-67
B:40-67
30
28
1.2
ENST00000263579
2
ENSE00001127770
chr11:
126176465-126176639
175
DCPS_HUMAN
68-126
59
2
A:68-126
B:68-126
59
59
1.3b
ENST00000263579
3b
ENSE00001202827
chr11:
126201300-126201445
146
DCPS_HUMAN
126-174
49
2
A:126-174
B:126-174
49
49
1.4b
ENST00000263579
4b
ENSE00000749617
chr11:
126208181-126208294
114
DCPS_HUMAN
175-212
38
2
A:175-212
B:175-212
38
38
1.5
ENST00000263579
5
ENSE00000749618
chr11:
126213202-126213312
111
DCPS_HUMAN
213-249
37
2
A:213-249
B:213-249
37
37
1.6b
ENST00000263579
6b
ENSE00002141498
chr11:
126215242-126215644
403
DCPS_HUMAN
250-337
88
2
A:250-337
B:250-336
88
87
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1st0a1 (A:146-337)
1b: SCOP_d1st0b1 (B:146-336)
2a: SCOP_d1st0a2 (A:38-145)
2b: SCOP_d1st0b2 (B:40-145)
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)
Protein Domains
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)
(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
HIT-like
(73)
Superfamily
:
HIT-like
(67)
Family
:
mRNA decapping enzyme DcpS C-terminal domain
(8)
Protein domain
:
mRNA decapping enzyme DcpS C-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1st0a1
A:146-337
1b
d1st0b1
B:146-336
Fold
:
mRNA decapping enzyme DcpS N-terminal domain
(8)
Superfamily
:
mRNA decapping enzyme DcpS N-terminal domain
(8)
Family
:
mRNA decapping enzyme DcpS N-terminal domain
(6)
Protein domain
:
mRNA decapping enzyme DcpS N-terminal domain
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1st0a2
A:38-145
2b
d1st0b2
B:40-145
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DcpS_C_1st0B01 (B:174-294)
1b: PFAM_DcpS_C_1st0B02 (B:174-294)
2a: PFAM_DcpS_1st0B03 (B:41-146)
2b: PFAM_DcpS_1st0B04 (B:41-146)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
HIT
(23)
Family
:
DcpS_C
(4)
Homo sapiens (Human)
(3)
1a
DcpS_C-1st0B01
B:174-294
1b
DcpS_C-1st0B02
B:174-294
Clan
:
no clan defined [family: DcpS]
(4)
Family
:
DcpS
(4)
Homo sapiens (Human)
(3)
2a
DcpS-1st0B03
B:41-146
2b
DcpS-1st0B04
B:41-146
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