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1QVJ
Asym. Unit
Info
Asym.Unit (60 KB)
Biol.Unit 1 (55 KB)
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(1)
Title
:
STRUCTURE OF NUDT9 COMPLEXED WITH RIBOSE-5-PHOSPHATE
Authors
:
B. W. Shen, A. -L. Perraud, A. S. Scharenberg, B. L. Stoddard
Date
:
27 Aug 03 (Deposition) - 16 Sep 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.91
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Nudix, Adprase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. W. Shen, A. -L. Perraud, A. S. Scharenberg, B. L. Stoddard
The Crystal Structure And Mutational Analysis Of Human Nudt
J. Mol. Biol. V. 332 385 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 14)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
3a: 5-O-PHOSPHONO-BETA-D-RIBOFURANOSE (RP5a)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
2
Ligand/Ion
MAGNESIUM ION
2
MSE
5
Mod. Amino Acid
SELENOMETHIONINE
3
RP5
1
Ligand/Ion
5-O-PHOSPHONO-BETA-D-RIBOFURANOSE
4
SO4
5
Ligand/Ion
SULFATE ION
5
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:91 , GLN A:92 , ASP A:93 , HOH A:377
BINDING SITE FOR RESIDUE SO4 A 555
2
AC2
SOFTWARE
GLN A:114 , ILE A:115 , SER A:116 , ARG A:146 , TRP A:165 , HOH A:390
BINDING SITE FOR RESIDUE SO4 A 556
3
AC3
SOFTWARE
GLU A:126 , LYS A:127 , LYS A:134
BINDING SITE FOR RESIDUE SO4 A 557
4
AC4
SOFTWARE
LYS A:203 , TRP A:210 , LYS A:308
BINDING SITE FOR RESIDUE SO4 A 558
5
AC5
SOFTWARE
LYS A:329 , TRP A:339 , HOH A:448
BINDING SITE FOR RESIDUE SO4 A 559
6
AC6
SOFTWARE
GLY A:214 , HOH A:443 , HOH A:549 , RP5 A:554 , MG A:561
BINDING SITE FOR RESIDUE MG A 560
7
AC7
SOFTWARE
GLU A:230 , HOH A:443 , HOH A:445 , HOH A:514 , MG A:560
BINDING SITE FOR RESIDUE MG A 561
8
AC8
SOFTWARE
TRP A:178 , LYS A:194 , HIS A:195 , ARG A:335 , ASP A:336 , HOH A:399
BINDING SITE FOR RESIDUE TRS A 553
9
AC9
SOFTWARE
ASP A:172 , SER A:183 , ARG A:204 , GLY A:215 , VAL A:269 , ASP A:271 , ARG A:273 , TYR A:321 , HIS A:324 , HOH A:388 , HOH A:428 , MG A:560
BINDING SITE FOR RESIDUE RP5 A 554
[
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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: NUDIX (A:178-334)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NUDIX
PS51462
Nudix hydrolase domain profile.
NUDT9_HUMAN
178-334
1
A:178-334
[
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Exons
(7, 7)
Info
All Exons
Exon 1.3b (A:59-116)
Exon 1.4 (A:116-148)
Exon 1.5a (A:148-177)
Exon 1.7 (A:177-214)
Exon 1.8b (A:215-263)
Exon 1.9b (A:264-292)
Exon 1.10b (A:292-350)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1a/1.3b
2: Boundary 1.3b/1.4
3: Boundary 1.4/1.5a
4: Boundary 1.5a/1.7
5: Boundary 1.7/1.8b
6: Boundary 1.8b/1.9b
7: Boundary 1.9b/1.10b
8: Boundary 1.10b/-
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
1.1a
ENST00000302174
1a
ENSE00001135449
chr4:
88343734-88344164
431
NUDT9_HUMAN
1-36
36
0
-
-
1.3b
ENST00000302174
3b
ENSE00001759594
chr4:
88356133-88356372
240
NUDT9_HUMAN
36-116
81
1
A:59-116
58
1.4
ENST00000302174
4
ENSE00001175754
chr4:
88359429-88359524
96
NUDT9_HUMAN
116-148
33
1
A:116-148
33
1.5a
ENST00000302174
5a
ENSE00001175744
chr4:
88362981-88363067
87
NUDT9_HUMAN
148-177
30
1
A:148-177
30
1.7
ENST00000302174
7
ENSE00001175734
chr4:
88370294-88370405
112
NUDT9_HUMAN
177-214
38
1
A:177-214
38
1.8b
ENST00000302174
8b
ENSE00001175727
chr4:
88372741-88372887
147
NUDT9_HUMAN
215-263
49
1
A:215-263
49
1.9b
ENST00000302174
9b
ENSE00001175718
chr4:
88375523-88375607
85
NUDT9_HUMAN
264-292
29
1
A:264-292
29
1.10b
ENST00000302174
10b
ENSE00001556821
chr4:
88378995-88379497
503
NUDT9_HUMAN
292-350
59
1
A:292-350
59
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1qvja_ (A:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nudix
(141)
Superfamily
:
Nudix
(141)
Family
:
MutT-like
(82)
Protein domain
:
NUDT9 (mitochondrial ADP-ribose pyrophosphatase)
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1qvja_
A:
[
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]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1qvjA02 (A:169-269,A:281-350)
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Classes
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)
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)
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)
(
)
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Nucleoside Triphosphate Pyrophosphohydrolase
(89)
Homologous Superfamily
:
Nucleoside Triphosphate Pyrophosphohydrolase
(89)
Human (Homo sapiens)
(6)
1a
1qvjA02
A:169-269,A:281-350
[
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]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_NUDIX_1qvjA01 (A:181-334)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NUDIX
(85)
Family
:
NUDIX
(78)
Homo sapiens (Human)
(12)
1a
NUDIX-1qvjA01
A:181-334
[
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]
Atom Selection
(currently selected atoms:
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Protein
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Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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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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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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