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Getting 'Exon' information from database.
3V7K
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
CO-CRYSTAL STRUCTURE OF K72E VARIANT OF RAT POLYMERASE BETA: ENZYME-DNA BINARY COMPLEX
Authors
:
S. Rangarajan, J. Jaeger
Date
:
21 Dec 11 (Deposition) - 16 Jan 13 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.27
Chains
:
Asym. Unit : A,P,T
Biol. Unit 1: A,P,T (1x)
Keywords
:
Protein-Dna Complex, Repair Polymerase, Transferase-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Rangarajan, C. L. Gridley, S. Firbank, S. Dalal, J. B. Sweasy, J. Jaeger
Crystallographic Studies Of K72E Mutant Dna Polymerase Explain Loss Of Lyase Function And Reveal Changes In The Overall Conformational State Of The Polymerase Domain
To Be Published
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
1c: SODIUM ION (NAc)
1d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
4
Ligand/Ion
SODIUM ION
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:190
BINDING SITE FOR RESIDUE NA A 401
2
AC2
SOFTWARE
ASP A:190
BINDING SITE FOR RESIDUE NA A 402
3
AC3
SOFTWARE
THR A:101 , ILE A:106 , DG P:6
BINDING SITE FOR RESIDUE NA A 404
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:179-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DNA_POLYMERASE_X
PS00522
DNA polymerase family X signature.
DPOLB_RAT
179-198
1
A:179-198
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Exons
(14, 14)
Info
All Exons
Exon 1.1 (A:5-21)
Exon 1.2 (A:21-40)
Exon 1.3 (A:40-62)
Exon 1.4 (A:63-87)
Exon 1.5 (A:88-107)
Exon 1.6 (A:107-124)
Exon 1.7 (A:124-141)
Exon 1.8 (A:141-159)
Exon 1.9 (A:160-184)
Exon 1.10 (A:184-207)
Exon 1.11 (A:208-236)
Exon 1.12 (A:237-258)
Exon 1.13 (A:258-305)
Exon 1.14 (A:305-335)
View:
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All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/-
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
1.1
ENSRNOT00000026039
1
ENSRNOE00000186777
chr16:
73864707-73864774
68
DPOLB_RAT
1-21
21
1
A:5-21
17
1.2
ENSRNOT00000026039
2
ENSRNOE00000185461
chr16:
73864965-73865022
58
DPOLB_RAT
21-40
20
1
A:21-40
20
1.3
ENSRNOT00000026039
3
ENSRNOE00000185504
chr16:
73867557-73867623
67
DPOLB_RAT
40-62
23
1
A:40-62
23
1.4
ENSRNOT00000026039
4
ENSRNOE00000185543
chr16:
73869319-73869393
75
DPOLB_RAT
63-87
25
1
A:63-87
25
1.5
ENSRNOT00000026039
5
ENSRNOE00000186057
chr16:
73870085-73870143
59
DPOLB_RAT
88-107
20
1
A:88-107
20
1.6
ENSRNOT00000026039
6
ENSRNOE00000185607
chr16:
73871161-73871210
50
DPOLB_RAT
107-124
18
1
A:107-124
18
1.7
ENSRNOT00000026039
7
ENSRNOE00000185647
chr16:
73873715-73873766
52
DPOLB_RAT
124-141
18
1
A:124-141
18
1.8
ENSRNOT00000026039
8
ENSRNOE00000186149
chr16:
73875864-73875918
55
DPOLB_RAT
141-159
19
1
A:141-159
19
1.9
ENSRNOT00000026039
9
ENSRNOE00000186214
chr16:
73876001-73876073
73
DPOLB_RAT
160-184
25
1
A:160-184
25
1.10
ENSRNOT00000026039
10
ENSRNOE00000185711
chr16:
73876683-73876753
71
DPOLB_RAT
184-207
24
1
A:184-207
24
1.11
ENSRNOT00000026039
11
ENSRNOE00000185748
chr16:
73878874-73878960
87
DPOLB_RAT
208-236
29
1
A:208-236
29
1.12
ENSRNOT00000026039
12
ENSRNOE00000185778
chr16:
73884550-73884614
65
DPOLB_RAT
237-258
22
1
A:237-258
22
1.13
ENSRNOT00000026039
13
ENSRNOE00000186274
chr16:
73885616-73885755
140
DPOLB_RAT
258-305
48
1
A:258-305
48
1.14
ENSRNOT00000026039
14
ENSRNOE00000235677
chr16:
73887775-73890113
2339
DPOLB_RAT
305-335
31
1
A:305-335
31
[
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SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3v7ka1 (A:5-91)
2a: SCOP_d3v7ka2 (A:92-148)
3a: SCOP_d3v7ka3 (A:149-335)
View:
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Folds
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
SAM domain-like
(639)
Superfamily
:
DNA polymerase beta, N-terminal domain-like
(205)
Family
:
DNA polymerase beta, N-terminal domain-like
(183)
Protein domain
:
DNA polymerase beta, N-terminal (8 kD)-domain
(156)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(15)
1a
d3v7ka1
A:5-91
Superfamily
:
PsbU/PolX domain-like
(218)
Family
:
DNA polymerase beta-like, second domain
(190)
Protein domain
:
DNA polymerase beta
(164)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(23)
2a
d3v7ka2
A:92-148
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nucleotidyltransferase
(287)
Superfamily
:
Nucleotidyltransferase
(287)
Family
:
DNA polymerase beta-like
(218)
Protein domain
:
DNA polymerase beta, catalytic (31 kD) fragment
(164)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(23)
3a
d3v7ka3
A:149-335
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain T
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (136 KB)
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