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Getting 'Exon' information from database.
2GDZ
Asym. Unit
Info
Asym.Unit (54 KB)
Biol.Unit 1 (97 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 15-HYDROXYPROSTAGLANDIN DEHYDROGENASE TYPE1, COMPLEXED WITH NAD+
Authors
:
E. S. Pilka, K. Guo, K. Kavanagh, F. Von Delft, C. Arrowsmith, J. Weigel A. Edwards, M. Sundstrom, U. Oppermann, Structural Genomics Conso (Sgc)
Date
:
17 Mar 06 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Hydroxyprostaglandin, Dehydrogenase, Structural Genomics, Short-Chain Dehydrogenase/Reductase, Inflammation, Structural Genomics Consortium, Sgc, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
F. H. Niesen, L. Schultz, A. Jadhav, C. Bhatia, K. Guo, D. J. Maloney, E. S. Pilka, M. Wang, U. Oppermann, T. D. Heightman, A. Simeonov
High-Affinity Inhibitors Of Human Nad-Dependent 15-Hydroxyprostaglandin Dehydrogenase: Mechanisms Of Inhibition And Structure-Activity Relationships.
Plos One V. 5 E1371 2010
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
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Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:12 , GLN A:15 , GLY A:16 , ILE A:17 , ASP A:36 , TRP A:37 , CYS A:63 , ASP A:64 , VAL A:65 , ASN A:91 , ALA A:92 , GLY A:93 , VAL A:94 , ILE A:106 , SER A:137 , SER A:138 , TYR A:151 , LYS A:155 , PRO A:183 , GLY A:184 , PHE A:185 , VAL A:186 , THR A:188 , ALA A:189 , ILE A:190 , HOH A:304 , HOH A:313 , HOH A:325 , HOH A:378 , HOH A:383 , HOH A:434 , HOH A:441
BINDING SITE FOR RESIDUE NAD A 300
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_046209 (A140P, chain A, )
2: VAR_060792 (S193P, chain A, )
3: VAR_006972 (Y217C, chain A, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_046209
A
140
P
PGDH_HUMAN
Disease (COA)
---
A
A
140
P
2
UniProt
VAR_060792
S
193
P
PGDH_HUMAN
Disease (ICNC)
---
A
S
193
P
3
UniProt
VAR_006972
Y
217
C
PGDH_HUMAN
Polymorphism
---
A
Y
217
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ADH_SHORT (A:138-166)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADH_SHORT
PS00061
Short-chain dehydrogenases/reductases family signature.
PGDH_HUMAN
138-166
1
A:138-166
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Exons
(7, 7)
Info
All Exons
Exon 1.1c (A:1-31)
Exon 1.2b (A:32-73)
Exon 1.3 (A:73-108)
Exon 1.4 (A:109-141)
Exon 1.6b (A:141-166)
Exon 1.7d (A:167-221)
Exon 1.8h (A:221-265 (gaps))
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All Exon Boundaries
1: Boundary -/1.1c
2: Boundary 1.1c/1.2b
3: Boundary 1.2b/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.6b
6: Boundary 1.6b/1.7d
7: Boundary 1.7d/1.8h
8: Boundary 1.8h/-
View:
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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
1.1c
ENST00000296522
1c
ENSE00002054104
chr4:
175444049-175443510
540
PGDH_HUMAN
1-31
31
1
A:1-31
31
1.2b
ENST00000296522
2b
ENSE00001081620
chr4:
175443218-175443095
124
PGDH_HUMAN
32-73
42
1
A:32-73
42
1.3
ENST00000296522
3
ENSE00001081626
chr4:
175439228-175439122
107
PGDH_HUMAN
73-108
36
1
A:73-108
36
1.4
ENST00000296522
4
ENSE00001081624
chr4:
175429943-175429847
97
PGDH_HUMAN
109-141
33
1
A:109-141
33
1.6b
ENST00000296522
6b
ENSE00001081622
chr4:
175416775-175416699
77
PGDH_HUMAN
141-166
26
1
A:141-166
26
1.7d
ENST00000296522
7d
ENSE00001081619
chr4:
175414465-175414302
164
PGDH_HUMAN
167-221
55
1
A:167-221
55
1.8h
ENST00000296522
8h
ENSE00001763478
chr4:
175413245-175411328
1918
PGDH_HUMAN
221-266
46
1
A:221-265 (gaps)
46
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2gdza1 (A:3-256)
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Protein Domains
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Organisms
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(
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Tyrosine-dependent oxidoreductases
(503)
Protein domain
:
15-hydroxyprostaglandin dehydrogenase, PGDH
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d2gdza1
A:3-256
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Chain A
Asymmetric Unit 1
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