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1HUZ
Asym. Unit
Info
Asym.Unit (128 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DNA POLYMERASE COMPLEXED WITH DNA AND CR-PCP
Authors
:
J. W. Arndt, W. Gong, X. Zhong, A. K. Showalter, J. Liu, Z. Lin, C. Paxson, M. -D. Tsai, M. K. Chan
Date
:
04 Jan 01 (Deposition) - 23 Apr 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,P,T
Biol. Unit 1: A,P,T (1x)
Biol. Unit 2: B,C,D (1x)
Keywords
:
Protein-Dna Complex, Transferase/Dna Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
J. W. Arndt, W. Gong, X. Zhong, A. K. Showalter, J. Liu, C. A. Dunlap, Z. Lin, C. Paxson, M. D. Tsai, M. K. Chan
Insight Into The Catalytic Mechanism Of Dna Polymerase Beta: Structures Of Intermediate Complexes.
Biochemistry V. 40 5368 2001
(for further references see the
PDB file header
)
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Hetero Components
(2, 4)
Info
All Hetero Components
1a: CHROMIUM ION (CRa)
1b: CHROMIUM ION (CRb)
2a: METHYLENEDIPHOSPHONIC ACID (MDNa)
2b: METHYLENEDIPHOSPHONIC ACID (MDNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CR
2
Ligand/Ion
CHROMIUM ION
2
MDN
2
Ligand/Ion
METHYLENEDIPHOSPHONIC ACID
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:190 , ASP A:192 , MDN A:338 , DT P:8
BINDING SITE FOR RESIDUE CR A 999
2
AC2
SOFTWARE
ASP B:190 , ASP B:192 , MDN B:338 , DT D:8
BINDING SITE FOR RESIDUE CR B 999
3
AC3
SOFTWARE
GLY A:179 , SER A:180 , ARG A:183 , GLY A:189 , ASP A:190 , ASP A:192 , CR A:999 , HOH A:1005 , DT P:8
BINDING SITE FOR RESIDUE MDN A 338
4
AC4
SOFTWARE
ARG B:149 , GLY B:179 , SER B:180 , ARG B:183 , SER B:188 , GLY B:189 , ASP B:190 , ASP B:192 , CR B:999 , HOH B:1005 , HOH B:1039 , DT D:8
BINDING SITE FOR RESIDUE MDN B 338
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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, 2)
Info
All PROSITE Patterns/Profiles
1: DNA_POLYMERASE_X (A:179-198,B: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
2
A:179-198
B:179-198
[
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Exons
(14, 28)
Info
All Exons
Exon 1.1 (A:10-21 | B:10-21)
Exon 1.2 (A:21-40 | B:21-40)
Exon 1.3 (A:40-62 | B:40-62)
Exon 1.4 (A:63-87 | B:63-87)
Exon 1.5 (A:88-107 | B:88-107)
Exon 1.6 (A:107-124 | B:107-124)
Exon 1.7 (A:124-141 | B:124-141)
Exon 1.8 (A:141-159 | B:141-159)
Exon 1.9 (A:160-184 | B:160-184)
Exon 1.10 (A:184-207 | B:184-207)
Exon 1.11 (A:208-236 | B:208-236)
Exon 1.12 (A:237-258 | B:237-258)
Exon 1.13 (A:258-305 | B:258-305)
Exon 1.14 (A:305-334 | B:305-334)
View:
Select:
Label:
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
2
A:10-21
B:10-21
12
12
1.2
ENSRNOT00000026039
2
ENSRNOE00000185461
chr16:
73864965-73865022
58
DPOLB_RAT
21-40
20
2
A:21-40
B:21-40
20
20
1.3
ENSRNOT00000026039
3
ENSRNOE00000185504
chr16:
73867557-73867623
67
DPOLB_RAT
40-62
23
2
A:40-62
B:40-62
23
23
1.4
ENSRNOT00000026039
4
ENSRNOE00000185543
chr16:
73869319-73869393
75
DPOLB_RAT
63-87
25
2
A:63-87
B:63-87
25
25
1.5
ENSRNOT00000026039
5
ENSRNOE00000186057
chr16:
73870085-73870143
59
DPOLB_RAT
88-107
20
2
A:88-107
B:88-107
20
20
1.6
ENSRNOT00000026039
6
ENSRNOE00000185607
chr16:
73871161-73871210
50
DPOLB_RAT
107-124
18
2
A:107-124
B:107-124
18
18
1.7
ENSRNOT00000026039
7
ENSRNOE00000185647
chr16:
73873715-73873766
52
DPOLB_RAT
124-141
18
2
A:124-141
B:124-141
18
18
1.8
ENSRNOT00000026039
8
ENSRNOE00000186149
chr16:
73875864-73875918
55
DPOLB_RAT
141-159
19
2
A:141-159
B:141-159
19
19
1.9
ENSRNOT00000026039
9
ENSRNOE00000186214
chr16:
73876001-73876073
73
DPOLB_RAT
160-184
25
2
A:160-184
B:160-184
25
25
1.10
ENSRNOT00000026039
10
ENSRNOE00000185711
chr16:
73876683-73876753
71
DPOLB_RAT
184-207
24
2
A:184-207
B:184-207
24
24
1.11
ENSRNOT00000026039
11
ENSRNOE00000185748
chr16:
73878874-73878960
87
DPOLB_RAT
208-236
29
2
A:208-236
B:208-236
29
29
1.12
ENSRNOT00000026039
12
ENSRNOE00000185778
chr16:
73884550-73884614
65
DPOLB_RAT
237-258
22
2
A:237-258
B:237-258
22
22
1.13
ENSRNOT00000026039
13
ENSRNOE00000186274
chr16:
73885616-73885755
140
DPOLB_RAT
258-305
48
2
A:258-305
B:258-305
48
48
1.14
ENSRNOT00000026039
14
ENSRNOE00000235677
chr16:
73887775-73890113
2339
DPOLB_RAT
305-335
31
2
A:305-334
B:305-334
30
30
[
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]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1huza1 (A:10-91)
1b: SCOP_d1huzb1 (B:10-91)
2a: SCOP_d1huza3 (A:92-148)
2b: SCOP_d1huzb3 (B:92-148)
3a: SCOP_d1huza4 (A:149-334)
3b: SCOP_d1huzb4 (B:149-334)
View:
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(
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)
(
)
Families
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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
d1huza1
A:10-91
1b
d1huzb1
B:10-91
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
d1huza3
A:92-148
2b
d1huzb3
B: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
d1huza4
A:149-334
3b
d1huzb4
B:149-334
[
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1huzA03 (A:149-271)
1b: CATH_1huzB03 (B:149-271)
2a: CATH_1huzA04 (A:272-334)
2b: CATH_1huzB04 (B:272-334)
3a: CATH_1huzA01 (A:10-91)
3b: CATH_1huzB01 (B:10-91)
4a: CATH_1huzA02 (A:92-148)
4b: CATH_1huzB02 (B:92-148)
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(
)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta Polymerase; domain 2
(187)
Homologous Superfamily
:
Beta Polymerase, domain 2
(183)
[unclassified]
(117)
1a
1huzA03
A:149-271
1b
1huzB03
B:149-271
Topology
:
Beta Polymerase; domain 3
(161)
Homologous Superfamily
:
Beta Polymerase, domain 3
(161)
[unclassified]
(116)
2a
1huzA04
A:272-334
2b
1huzB04
B:272-334
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
[code=1.10.150.110, no name defined]
(150)
[unclassified]
(116)
3a
1huzA01
A:10-91
3b
1huzB01
B:10-91
Homologous Superfamily
:
5' to 3' exonuclease, C-terminal subdomain
(384)
[unclassified]
(230)
4a
1huzA02
A:92-148
4b
1huzB02
B:92-148
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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Protein & NOT PROSITE
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Chain C
Chain D
Chain P
Chain T
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