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Getting 'Exon' information from database.
2I7D
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (155 KB)
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(1)
Title
:
STRUCTURE OF HUMAN CYTOSOLIC DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH DEOXYURIDINE, ALF4 AND MG2+
Authors
:
A. Rinaldo-Matthis, K. Wallden, P. Nordlund
Date
:
30 Aug 06 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Deoxyribonucleotidase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Wallden, A. Rinaldo-Matthis, B. Ruzzenente, C. Rampazzo, V. Bianchi, P. Nordlund
Structures Of Human And Murine Cytosolic Deoxyribonucleotidase: Insights Into Substrate Specificity And Catalysis
To Be Published
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: TETRAFLUOROALUMINATE ION (ALFa)
1b: TETRAFLUOROALUMINATE ION (ALFb)
2a: 2'-DEOXYURIDINE (DURa)
2b: 2'-DEOXYURIDINE (DURb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALF
2
Ligand/Ion
TETRAFLUOROALUMINATE ION
2
DUR
2
Ligand/Ion
2'-DEOXYURIDINE
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:10 , ASP A:12 , ASP A:145 , ALF A:400 , HOH A:729 , HOH A:731
BINDING SITE FOR RESIDUE MG A 728
2
AC2
SOFTWARE
ASP B:10 , ASP B:12 , ASP B:145 , ALF B:401 , HOH B:730 , HOH B:733
BINDING SITE FOR RESIDUE MG B 729
3
AC3
SOFTWARE
ASP A:10 , MET A:11 , ASP A:12 , THR A:99 , SER A:100 , LYS A:112 , LYS A:134 , DUR A:300 , MG A:728 , HOH A:729 , HOH A:731
BINDING SITE FOR RESIDUE ALF A 400
4
AC4
SOFTWARE
ASP B:10 , MET B:11 , ASP B:12 , THR B:99 , SER B:100 , LYS B:112 , LYS B:134 , DUR B:301 , MG B:729 , HOH B:730 , HOH B:733
BINDING SITE FOR RESIDUE ALF B 401
5
AC5
SOFTWARE
ASP A:12 , PHE A:18 , PHE A:44 , LEU A:45 , ALA A:46 , SER A:100 , PRO A:101 , LEU A:102 , ALF A:400 , HOH A:731 , HOH A:759 , HOH A:782 , HOH A:821 , HOH A:859
BINDING SITE FOR RESIDUE DUR A 300
6
AC6
SOFTWARE
ASP B:12 , PHE B:18 , PHE B:44 , LEU B:45 , ALA B:46 , SER B:100 , PRO B:101 , LEU B:102 , ALF B:401 , HOH B:733 , HOH B:737 , HOH B:771 , HOH B:821 , HOH B:878
BINDING SITE FOR RESIDUE DUR B 301
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_048102 (P68L, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_048102
P
68
L
NT5C_HUMAN
Polymorphism
11541956
A/B
P
68
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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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
(5, 10)
Info
All Exons
Exon 1.1 (A:3-58 | B:4-58)
Exon 1.2 (A:59-92 | B:59-92)
Exon 1.3 (A:92-112 | B:92-112)
Exon 1.4 (A:113-151 | B:113-151)
Exon 1.5 (A:151-195 | B:151-195)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/-
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
ENST00000245552
1
ENSE00001174732
chr17:
73127877-73127629
249
NT5C_HUMAN
1-58
58
2
A:3-58
B:4-58
56
55
1.2
ENST00000245552
2
ENSE00000744347
chr17:
73127376-73127276
101
NT5C_HUMAN
59-92
34
2
A:59-92
B:59-92
34
34
1.3
ENST00000245552
3
ENSE00000744348
chr17:
73127200-73127140
61
NT5C_HUMAN
92-112
21
2
A:92-112
B:92-112
21
21
1.4
ENST00000245552
4
ENSE00000744349
chr17:
73126962-73126848
115
NT5C_HUMAN
113-151
39
2
A:113-151
B:113-151
39
39
1.5
ENST00000245552
5
ENSE00001174725
chr17:
73126737-73126324
414
NT5C_HUMAN
151-201
51
2
A:151-195
B:151-195
45
45
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2i7da_ (A:)
1b: SCOP_d2i7db_ (B:)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
5'(3')-deoxyribonucleotidase (dNT-2)
(18)
Protein domain
:
automated matches
(14)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d2i7da_
A:
1b
d2i7db_
B:
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2i7dA01 (A:3-17,A:73-195)
1b: CATH_2i7dB01 (B:4-17,B:73-195)
2a: CATH_2i7dA02 (A:18-72)
2b: CATH_2i7dB02 (B:18-72)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Human (Homo sapiens)
(42)
1a
2i7dA01
A:3-17,A:73-195
1b
2i7dB01
B:4-17,B:73-195
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase Protein R1; domain 1
(62)
Homologous Superfamily
:
Deoxyribonucleotidase; domain 2
(16)
Human (Homo sapiens)
(13)
2a
2i7dA02
A:18-72
2b
2i7dB02
B:18-72
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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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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Asym.Unit (159 KB)
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