PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2VOM
Biol. Unit 1
Info
Asym.Unit (166 KB)
Biol.Unit 1 (84 KB)
Biol.Unit 2 (82 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE DEFICIENCY. MUTATION E104D AND CORRELATION TO SOLVENT PERTURBATION.
Authors
:
C. Rodriguez-Almazan, R. Arreola-Alemon, D. Rodriguez-Larrea, B. Aguirre-Lopez, M. T. De Gomez-Puyou, R. Perez-Montfort, M. Costas, A. Gomez-Puyou, A. Torres-Larios
Date
:
19 Feb 08 (Deposition) - 17 Jun 08 (Release) - 29 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Isomerase, Alternative Splicing, Fatty Acid Biosynthesis, Lipid Synthesis, Disease Mutation, Pentose Shunt, Phosphoprotein, Gluconeogenesis, Glycolysis, Acetylation, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Rodriguez-Almazan, R. Arreola-Alemon, D. Rodriguez-Larrea, B. Aguirre-Lopez, M. T. De Gomez-Puyou, R. Perez-Montfort, M. Costas, A. Gomez-Puyou, A. Torres-Larios
Structural Basis Of Human Triosephosphate Isomerase Deficiency: Mutation E104D Is Related To Alterations Of A Conserved Water Network At The Dimer Interface.
J. Biol. Chem. V. 283 23254 2008
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(8, 16)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_007534 (C41Y, chain A/B, )
2: VAR_007535 (G72A, chain A/B, )
3: VAR_007536 (D104D, chain A/B, )
4: VAR_007537 (G122R, chain A/B, )
5: VAR_007538 (V154M, chain A/B, )
6: VAR_007539 (I170V, chain A/B, )
7: VAR_007540 (V231M, chain A/B, )
8: VAR_007541 (F240L, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_007534
C
79
Y
TPIS_HUMAN
Disease (TPID)
---
A/B
C
41
Y
2
UniProt
VAR_007535
G
110
A
TPIS_HUMAN
Disease (TPID)
---
A/B
G
72
A
3
UniProt
VAR_007536
E
142
D
TPIS_HUMAN
Disease (TPID)
---
A/B
D
104
D
4
UniProt
VAR_007537
G
160
R
TPIS_HUMAN
Unclassified
---
A/B
G
122
R
5
UniProt
VAR_007538
V
192
M
TPIS_HUMAN
Disease (TPID)
188138723
A/B
V
154
M
6
UniProt
VAR_007539
I
208
V
TPIS_HUMAN
Disease (TPID)
---
A/B
I
170
V
7
UniProt
VAR_007540
V
269
M
TPIS_HUMAN
Disease (TPID)
---
A/B
V
231
M
8
UniProt
VAR_007541
F
278
L
TPIS_HUMAN
Disease (TPID)
---
A/B
F
240
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: TIM_2 (A:5-246,B:5-246)
2: TIM_1 (A:163-173,B:163-173)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TIM_2
PS51440
Triosephosphate isomerase (TIM) family profile.
TPIS_HUMAN
43-284
2
A:5-246
B:5-246
-
-
2
TIM_1
PS00171
Triosephosphate isomerase active site.
TPIS_HUMAN
201-211
2
A:163-173
B:163-173
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2voma_ (A:)
1b: SCOP_d2vomb_ (B:)
1c: SCOP_d2vomc_ (C:)
1d: SCOP_d2vomd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Triosephosphate isomerase (TIM)
(148)
Family
:
Triosephosphate isomerase (TIM)
(128)
Protein domain
:
Triosephosphate isomerase
(126)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2voma_
A:
1b
d2vomb_
B:
1c
d2vomc_
C:
1d
d2vomd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2vomB00 (B:3-248)
1b: CATH_2vomA00 (A:4-248)
1c: CATH_2vomC00 (C:3-247)
1d: CATH_2vomD00 (D:4-245)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Human (Homo sapiens)
(78)
1a
2vomB00
B:3-248
1b
2vomA00
A:4-248
1c
2vomC00
C:3-247
1d
2vomD00
D:4-245
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
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)
[
close Script example commands
]
Log
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (166 KB)
Header - Asym.Unit
Biol.Unit 1 (84 KB)
Header - Biol.Unit 1
Biol.Unit 2 (82 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2VOM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help