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1Q78
Asym. Unit
Info
Asym.Unit (86 KB)
Biol.Unit 1 (82 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF POLY(A) POLYMERASE IN COMPLEX WITH 3'-DATP AND MAGNESIUM CHLORIDE
Authors
:
G. Martin, A. Moglich, W. Keller, S. Doublie
Date
:
16 Aug 03 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Mrna Processing, Nucleotidyl Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Martin, A. Moglich, W. Keller, S. Doublie
Biochemical And Structural Insights Into Substrate Binding And Catalytic Mechanism Of Mammalian Poly(A) Polymerase.
J. Mol. Biol. V. 341 911 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE (3ATa)
2a: 3-SULFINOALANINE (CSDa)
2b: 3-SULFINOALANINE (CSDb)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3AT
1
Ligand/Ion
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
2
CSD
2
Mod. Amino Acid
3-SULFINOALANINE
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:113 , ASP A:115 , 3AT A:1000
BINDING SITE FOR RESIDUE MG A 1002
2
AC2
SOFTWARE
PHE A:100 , GLY A:101 , SER A:102 , ASP A:115 , ASN A:202 , VAL A:206 , LYS A:228 , TYR A:237 , GLY A:246 , VAL A:247 , THR A:317 , MG A:1002 , HOH A:2043 , HOH A:2050 , HOH A:2060 , HOH A:2069 , HOH A:2108 , HOH A:2117
BINDING SITE FOR RESIDUE 3AT A 1000
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(15, 15)
Info
All Exons
Exon 1.2 (A:19-61)
Exon 1.3 (A:61-83)
Exon 1.4 (A:84-111)
Exon 1.5 (A:111-147)
Exon 1.6 (A:148-165)
Exon 1.7 (A:166-203)
Exon 1.8 (A:203-233)
Exon 1.9 (A:233-279)
Exon 1.10 (A:279-303)
Exon 1.11 (A:304-344)
Exon 1.12 (A:344-372)
Exon 1.13 (A:372-390)
Exon 1.14 (A:390-430)
Exon 1.15 (A:430-467 (gaps))
Exon 1.16 (A:467-498)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.2
02: Boundary 1.2/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16
16: Boundary 1.16/1.17
View:
Label:
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
1.1b
ENSBTAT00000005300
1b
ENSBTAE00000429997
chr21:
61558615-61558668
54
PAPOA_BOVIN
1-3
3
0
-
-
1.2
ENSBTAT00000005300
2
ENSBTAE00000392174
chr21:
61572974-61573147
174
PAPOA_BOVIN
3-61
59
1
A:19-61
43
1.3
ENSBTAT00000005300
3
ENSBTAE00000042583
chr21:
61573550-61573616
67
PAPOA_BOVIN
61-83
23
1
A:61-83
23
1.4
ENSBTAT00000005300
4
ENSBTAE00000042584
chr21:
61576385-61576466
82
PAPOA_BOVIN
84-111
28
1
A:84-111
28
1.5
ENSBTAT00000005300
5
ENSBTAE00000042586
chr21:
61578210-61578319
110
PAPOA_BOVIN
111-147
37
1
A:111-147
37
1.6
ENSBTAT00000005300
6
ENSBTAE00000042587
chr21:
61578770-61578823
54
PAPOA_BOVIN
148-165
18
1
A:148-165
18
1.7
ENSBTAT00000005300
7
ENSBTAE00000042589
chr21:
61581599-61581710
112
PAPOA_BOVIN
166-203
38
1
A:166-203
38
1.8
ENSBTAT00000005300
8
ENSBTAE00000042592
chr21:
61582361-61582450
90
PAPOA_BOVIN
203-233
31
1
A:203-233
31
1.9
ENSBTAT00000005300
9
ENSBTAE00000042594
chr21:
61582541-61582679
139
PAPOA_BOVIN
233-279
47
1
A:233-279
47
1.10
ENSBTAT00000005300
10
ENSBTAE00000381557
chr21:
61584527-61584599
73
PAPOA_BOVIN
279-303
25
1
A:279-303
25
1.11
ENSBTAT00000005300
11
ENSBTAE00000042601
chr21:
61585936-61586056
121
PAPOA_BOVIN
304-344
41
1
A:304-344
41
1.12
ENSBTAT00000005300
12
ENSBTAE00000042603
chr21:
61587008-61587092
85
PAPOA_BOVIN
344-372
29
1
A:344-372
29
1.13
ENSBTAT00000005300
13
ENSBTAE00000042606
chr21:
61591631-61591684
54
PAPOA_BOVIN
372-390
19
1
A:372-390
19
1.14
ENSBTAT00000005300
14
ENSBTAE00000042609
chr21:
61592212-61592331
120
PAPOA_BOVIN
390-430
41
1
A:390-430
41
1.15
ENSBTAT00000005300
15
ENSBTAE00000042612
chr21:
61593451-61593560
110
PAPOA_BOVIN
430-467
38
1
A:430-467 (gaps)
38
1.16
ENSBTAT00000005300
16
ENSBTAE00000042616
chr21:
61595973-61596094
122
PAPOA_BOVIN
467-507
41
1
A:467-498
32
1.17
ENSBTAT00000005300
17
ENSBTAE00000042620
chr21:
61599064-61599206
143
PAPOA_BOVIN
508-555
48
0
-
-
1.18
ENSBTAT00000005300
18
ENSBTAE00000246874
chr21:
61601533-61601633
101
PAPOA_BOVIN
555-589
35
0
-
-
1.19
ENSBTAT00000005300
19
ENSBTAE00000042630
chr21:
61601831-61602051
221
PAPOA_BOVIN
589-662
74
0
-
-
1.20
ENSBTAT00000005300
20
ENSBTAE00000042634
chr21:
61605738-61605800
63
PAPOA_BOVIN
663-683
21
0
-
-
1.21
ENSBTAT00000005300
21
ENSBTAE00000042636
chr21:
61607657-61607731
75
PAPOA_BOVIN
684-708
25
0
-
-
1.22a
ENSBTAT00000005300
22a
ENSBTAE00000378893
chr21:
61609752-61610065
314
PAPOA_BOVIN
709-739
31
0
-
-
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1q78a1 (A:215-364)
2a: SCOP_d1q78a3 (A:365-498)
3a: SCOP_d1q78a2 (A:19-214)
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(
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(
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Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
PAP/OAS1 substrate-binding domain
(46)
Superfamily
:
PAP/OAS1 substrate-binding domain
(46)
Family
:
Poly(A) polymerase, PAP, middle domain
(8)
Protein domain
:
Poly(A) polymerase, PAP, middle domain
(8)
Cow (Bos taurus) [TaxId: 9913]
(3)
1a
d1q78a1
A:215-364
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
PAP/Archaeal CCA-adding enzyme, C-terminal domain
(37)
Family
:
Poly(A) polymerase, PAP, C-terminal domain
(8)
Protein domain
:
Poly(A) polymerase, PAP, C-terminal domain
(8)
Cow (Bos taurus) [TaxId: 9913]
(3)
2a
d1q78a3
A:365-498
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
Poly(A) polymerase, PAP, N-terminal domain
(8)
Protein domain
:
Poly(A) polymerase, PAP, N-terminal domain
(8)
Cow (Bos taurus) [TaxId: 9913]
(3)
3a
d1q78a2
A:19-214
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1q78A01 (A:366-488)
2a: CATH_1q78A02 (A:53-208)
3a: CATH_1q78A03 (A:20-52,A:209-365)
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(
)
(
)
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.590, no name defined]
(8)
Cattle (Bos taurus)
(3)
1a
1q78A01
A:366-488
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
Cattle (Bos taurus)
(3)
2a
1q78A02
A:53-208
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Poly(a)-polymerase, middle domain
(9)
Homologous Superfamily
:
[code=1.10.1410.10, no name defined]
(8)
Cattle (Bos taurus)
(3)
3a
1q78A03
A:20-52,A:209-365
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_NTP_transf_2_1q78A01 (A:75-175)
2a: PFAM_PAP_RNA_bind_1q78A02 (A:366-498)
3a: PFAM_PAP_central_1q78A03 (A:19-365)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NTP_transf
(45)
Family
:
NTP_transf_2
(35)
Bos taurus (Bovine)
(1)
1a
NTP_transf_2-1q78A01
A:75-175
Clan
:
no clan defined [family: PAP_RNA-bind]
(3)
Family
:
PAP_RNA-bind
(3)
Bos taurus (Bovine)
(1)
2a
PAP_RNA-bind-1q78A02
A:366-498
Clan
:
no clan defined [family: PAP_central]
(3)
Family
:
PAP_central
(3)
Bos taurus (Bovine)
(1)
3a
PAP_central-1q78A03
A:19-365
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Asymmetric Unit 1
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