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2Q9P
Asym. Unit
Info
Asym.Unit (34 KB)
Biol.Unit 1 (29 KB)
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(1)
Title
:
HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 1, MG-F COMPLEX
Authors
:
A. G. Thorsell, R. Busam, C. H. Arrowsmith, H. Berglund, R. Collins, L. G. Dahlgren, A. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, L. Lehtio, M. Moche, P. Nordlund, T. Nyman, D. Ogg, J. Sagemark, M. Sundstrom, S. Van Den Berg, J. Weigelt, M. Welin, C. Persson, B. M. Hallberg, Structural Genomics Consortium (Sgc)
Date
:
13 Jun 07 (Deposition) - 11 Sep 07 (Release) - 25 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Diphosphoinositol Polyphosphate Phosphohydrolase, Nudix, Inositol Pyrophosphate Metabolism, Structural Genomics Consortium, Sgc
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Thorsell, C. Persson, S. Graslund, M. Hammarstrom, R. D. Busam, B. M. Hallberg
Crystal Structure Of Human Diphosphoinositol Phosphatase 1.
Proteins V. 77 242 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: FLUORIDE ION (Fa)
2b: FLUORIDE ION (Fb)
2c: FLUORIDE ION (Fc)
2d: FLUORIDE ION (Fd)
2e: FLUORIDE ION (Fe)
2f: FLUORIDE ION (Ff)
2g: FLUORIDE ION (Fg)
2h: FLUORIDE ION (Fh)
2i: FLUORIDE ION (Fi)
2j: FLUORIDE ION (Fj)
3a: INOSITOL HEXAKISPHOSPHATE (IHPa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
F
10
Ligand/Ion
FLUORIDE ION
3
IHP
1
Ligand/Ion
INOSITOL HEXAKISPHOSPHATE
4
MG
4
Ligand/Ion
MAGNESIUM ION
[
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Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:66 , GLU A:70 , IHP A:201 , MG A:302 , MG A:303 , MG A:304 , F A:403 , F A:405 , F A:409 , F A:410
BINDING SITE FOR RESIDUE MG A 301
02
AC2
SOFTWARE
GLY A:50 , GLY A:51 , GLU A:70 , IHP A:201 , MG A:301 , MG A:303 , F A:402 , F A:403 , F A:410
BINDING SITE FOR RESIDUE MG A 302
03
AC3
SOFTWARE
IHP A:201 , MG A:301 , MG A:302 , MG A:304 , F A:403 , F A:404 , F A:406 , F A:409 , F A:410 , HOH A:836 , HOH A:837
BINDING SITE FOR RESIDUE MG A 303
04
AC4
SOFTWARE
GLU A:66 , MG A:301 , MG A:303 , F A:404 , F A:406 , F A:407 , F A:408 , F A:409
BINDING SITE FOR RESIDUE MG A 304
05
AC5
SOFTWARE
SER A:28 , SER A:30 , GLU A:31 , GLU A:32 , GLU A:33 , HOH A:846
BINDING SITE FOR RESIDUE CL A 401
06
AC6
SOFTWARE
ILE A:47 , GLY A:50 , GLU A:70 , IHP A:201 , MG A:302 , HOH A:566
BINDING SITE FOR RESIDUE F A 402
07
AC7
SOFTWARE
GLY A:50 , GLY A:51 , GLU A:66 , GLU A:70 , IHP A:201 , MG A:301 , MG A:302 , MG A:303 , F A:404 , F A:409 , F A:410 , HOH A:837
BINDING SITE FOR RESIDUE F A 403
08
AC8
SOFTWARE
GLY A:51 , GLY A:52 , GLU A:66 , IHP A:201 , MG A:303 , MG A:304 , F A:403 , F A:406 , F A:407 , F A:409 , HOH A:821 , HOH A:836
BINDING SITE FOR RESIDUE F A 404
09
AC9
SOFTWARE
GLU A:66 , GLU A:69 , GLU A:70 , MG A:301 , F A:409 , F A:410 , HOH A:725
BINDING SITE FOR RESIDUE F A 405
10
BC1
SOFTWARE
MG A:303 , MG A:304 , F A:404 , F A:407 , F A:408 , F A:409 , HOH A:836
BINDING SITE FOR RESIDUE F A 406
11
BC2
SOFTWARE
GLY A:52 , ARG A:65 , GLU A:66 , MG A:304 , F A:404 , F A:406 , F A:408 , HOH A:637
BINDING SITE FOR RESIDUE F A 407
12
BC3
SOFTWARE
ARG A:65 , GLU A:66 , GLU A:69 , MG A:304 , F A:406 , F A:407 , F A:409 , HOH A:824
BINDING SITE FOR RESIDUE F A 408
13
BC4
SOFTWARE
GLU A:66 , MG A:301 , MG A:303 , MG A:304 , F A:403 , F A:404 , F A:405 , F A:406 , F A:408 , F A:410 , HOH A:612
BINDING SITE FOR RESIDUE F A 409
14
BC5
SOFTWARE
GLU A:70 , ARG A:115 , IHP A:201 , MG A:301 , MG A:302 , MG A:303 , F A:403 , F A:405 , F A:409 , HOH A:589 , HOH A:837
BINDING SITE FOR RESIDUE F A 410
15
BC6
SOFTWARE
ASN A:86 , GLN A:136
BINDING SITE FOR RESIDUE F A 411
16
BC7
SOFTWARE
ARG A:10 , LYS A:18 , ARG A:20 , SER A:39 , SER A:40 , ARG A:41 , ILE A:47 , GLY A:50 , GLY A:51 , GLY A:52 , GLU A:70 , ARG A:89 , HIS A:91 , ARG A:115 , LYS A:133 , MG A:301 , MG A:302 , MG A:303 , F A:402 , F A:403 , F A:404 , F A:410 , HOH A:602 , HOH A:606 , HOH A:738 , HOH A:803 , HOH A:821 , HOH A:836 , HOH A:837
BINDING SITE FOR RESIDUE IHP A 201
[
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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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NUDIX (A:17-141)
2: NUDIX_BOX (A:51-72)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NUDIX
PS51462
Nudix hydrolase domain profile.
NUDT3_HUMAN
17-142
1
A:17-141
2
NUDIX_BOX
PS00893
Nudix box signature.
NUDT3_HUMAN
51-72
1
A:51-72
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2q9pa_ (A:)
View:
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Classes
(
)
(
)
Folds
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)
Superfamilies
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(
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nudix
(141)
Superfamily
:
Nudix
(141)
Family
:
MutT-like
(82)
Protein domain
:
Diphosphoinositol polyphosphate phosphohydrolase
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2q9pa_
A:
[
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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)
Info
all PFAM domains
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Sorry, no Info available
[
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Atom Selection
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)
Protein
Nucleic
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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Miscellaneous
Script
Example Commands
Example Command
Action
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
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (34 KB)
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Header - Biol.Unit 1
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