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2Q66
Asym. Unit
Info
Asym.Unit (108 KB)
Biol.Unit 1 (102 KB)
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(1)
Title
:
STRUCTURE OF YEAST POLY(A) POLYMERASE WITH ATP AND OLIGO(A)
Authors
:
A. Bohm, P. Balbo
Date
:
04 Jun 07 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,X
Biol. Unit 1: A,X (1x)
Keywords
:
Protein Rna Complex Atp Polymerase Complex, Transferase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. B. Balbo, A. Bohm
Mechanism Of Poly(A) Polymerase: Structure Of The Enzyme-Mgatp-Rna Ternary Complex And Kinetic Analysis.
Structure V. 15 1117 2007
(for further references see the
PDB file header
)
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Hetero Components
(3, 19)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(19, 19)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:100 , ASP A:102 , ATP A:605 , HOH A:1097
BINDING SITE FOR RESIDUE MG A 602
02
AC2
SOFTWARE
TYR A:87 , GLY A:88 , SER A:89 , ASP A:100 , ASP A:102 , GLY A:190 , LYS A:215 , TYR A:224 , ASN A:226 , GLY A:233 , VAL A:234 , MET A:310 , ALA A:312 , MG A:602 , HOH A:727 , HOH A:817 , HOH A:872 , HOH A:880 , HOH A:896 , HOH A:919 , HOH A:920 , HOH A:966 , HOH A:1000 , HOH A:1088 , HOH A:1097 , A X:5
BINDING SITE FOR RESIDUE ATP A 605
03
AC3
SOFTWARE
LYS A:53 , GLN A:56 , GLU A:57 , GLN A:60 , TYR A:247 , ARG A:258 , ILE A:262 , HOH A:827 , HOH A:1142
BINDING SITE FOR RESIDUE EDO A 701
04
AC4
SOFTWARE
VAL A:16 , ALA A:250 , ARG A:258 , HOH A:820 , HOH A:911 , HOH A:980
BINDING SITE FOR RESIDUE EDO A 702
05
AC5
SOFTWARE
LYS A:34 , PHE A:39 , GLU A:418 , HOH A:733 , HOH A:755
BINDING SITE FOR RESIDUE EDO A 703
06
AC6
SOFTWARE
ASN A:23 , ASN A:26 , ASP A:27 , CYS A:251 , HOH A:805
BINDING SITE FOR RESIDUE EDO A 704
07
AC7
SOFTWARE
SER A:28 , SER A:344 , TRP A:345 , HOH A:921 , HOH A:1013
BINDING SITE FOR RESIDUE EDO A 705
08
AC8
SOFTWARE
PRO A:276 , ILE A:277 , HOH A:746 , HOH A:764
BINDING SITE FOR RESIDUE EDO A 706
09
AC9
SOFTWARE
GLU A:132 , ILE A:146 , LYS A:147 , HOH A:731 , HOH A:768
BINDING SITE FOR RESIDUE EDO A 707
10
BC1
SOFTWARE
GLN A:60 , TYR A:64 , ARG A:78 , GLY A:81
BINDING SITE FOR RESIDUE EDO A 708
11
BC2
SOFTWARE
A X:2
BINDING SITE FOR RESIDUE EDO X 709
12
BC3
SOFTWARE
LYS A:351 , LYS A:407 , PHE A:409 , VAL A:521 , ASP A:523 , HOH A:960 , HOH A:1018
BINDING SITE FOR RESIDUE EDO A 710
13
BC4
SOFTWARE
ARG A:221 , LYS A:351 , ASP A:353 , HOH A:1071
BINDING SITE FOR RESIDUE EDO A 711
14
BC5
SOFTWARE
GLU A:32 , GLU A:36 , ARG A:220 , ALA A:346 , PHE A:349 , GLU A:350
BINDING SITE FOR RESIDUE EDO A 712
15
BC6
SOFTWARE
VAL A:16 , GLY A:17 , ALA A:18 , ASP A:455
BINDING SITE FOR RESIDUE EDO A 713
16
BC7
SOFTWARE
VAL A:49 , LYS A:53 , GLU A:265 , ASN A:267 , HOH A:791 , HOH A:810 , HOH A:925
BINDING SITE FOR RESIDUE EDO A 714
17
BC8
SOFTWARE
ALA A:139 , PHE A:140 , HOH A:1054 , A X:4
BINDING SITE FOR RESIDUE EDO X 715
18
BC9
SOFTWARE
PHE A:470 , LYS A:478 , VAL A:479 , A X:1
BINDING SITE FOR RESIDUE EDO A 716
19
CC1
SOFTWARE
SER A:168 , VAL A:329 , HOH A:765 , HOH A:944
BINDING SITE FOR RESIDUE EDO A 717
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(1, 1)
Info
All Exons
Exon 1.1 (A:5-529 (gaps))
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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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
YKR002W
1
YKR002W.1
XI:442875-444581
1707
PAP_YEAST
1-568
568
1
A:5-529 (gaps)
525
[
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]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2q66a1 (A:202-351)
2a: SCOP_d2q66a3 (A:352-529)
3a: SCOP_d2q66a2 (A:5-201)
View:
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Classes
(
)
(
)
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(
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(
)
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)
(
)
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(
)
(
)
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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
1a
d2q66a1
A:202-351
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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
2a
d2q66a3
A:352-529
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)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(5)
3a
d2q66a2
A:5-201
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2q66A03 (A:353-521)
2a: CATH_2q66A02 (A:40-195)
3a: CATH_2q66A01 (A:5-39,A:196-352)
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)
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(
)
(
)
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)
[unclassified]
(1)
1a
2q66A03
A:353-521
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
[unclassified]
(117)
2a
2q66A02
A:40-195
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)
[unclassified]
(1)
3a
2q66A01
A:5-39,A:196-352
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_NTP_transf_2_2q66A01 (A:72-161)
2a: PFAM_PAP_RNA_bind_2q66A02 (A:353-529)
3a: PFAM_PAP_central_2q66A03 (A:5-352)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NTP_transf
(45)
Family
:
NTP_transf_2
(35)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(3)
1a
NTP_transf_2-2q66A01
A:72-161
Clan
:
no clan defined [family: PAP_RNA-bind]
(3)
Family
:
PAP_RNA-bind
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
2a
PAP_RNA-bind-2q66A02
A:353-529
Clan
:
no clan defined [family: PAP_central]
(3)
Family
:
PAP_central
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
3a
PAP_central-2q66A03
A:5-352
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