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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3ZYW
Asym. Unit
Info
Asym.Unit (51 KB)
Biol.Unit 1 (24 KB)
Biol.Unit 2 (24 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE FIRST GLUTAREDOXIN DOMAIN OF HUMAN GLUTAREDOXIN 3 (GLRX3)
Authors
:
M. Vollmar, C. Johansson, R. Cocking, T. Krojer, J. R. C. Muniz, K. L. Kav F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. Edwards, U. Oppermann
Date
:
29 Aug 11 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.84
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Vollmar, C. Johansson, R. Cocking, T. Krojer, J. R. C. Muniz, K. L. Kavanagh, F. Von Delft, C. Bountra, C. H. Arrowsmith, J. Weigelt A. Edwards, U. Oppermann
Crystal Structure Of The First Glutaredoxin Domain Of Human Glutaredoxin 3 (Glrx3)
To Be Published
[
close entry info
]
Hetero Components
(1, 5)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:208 , LEU A:209 , ILE A:210 , HOH A:2151 , LEU B:236 , PHE B:238 , GLN B:239
BINDING SITE FOR RESIDUE EDO A1240
2
AC2
SOFTWARE
THR A:141 , HIS A:142 , TYR A:194 , GLY A:207 , HOH A:2130
BINDING SITE FOR RESIDUE EDO A1241
3
AC3
SOFTWARE
PRO B:154 , HIS B:170 , PHE B:176 , EDO B:1242 , HOH B:2069 , HOH B:2077 , HOH B:2085 , HOH B:2204
BINDING SITE FOR RESIDUE EDO B1240
4
AC4
SOFTWARE
LYS B:139 , LEU B:140 , ALA B:143 , HOH B:2021 , HOH B:2089
BINDING SITE FOR RESIDUE EDO B1241
5
AC5
SOFTWARE
GLN B:155 , EDO B:1240 , HOH B:2037 , HOH B:2042 , HOH B:2204
BINDING SITE FOR RESIDUE EDO B1242
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: GLUTAREDOXIN_2 (A:134-232,B:134-232|A:233-238,B:23...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLUTAREDOXIN_2
PS51354
Glutaredoxin domain profile.
GLRX3_HUMAN
134-236
236-335
4
A:134-232
B:134-232
A:233-238
B:233-238
[
close PROSITE info
]
Exons
(4, 8)
Info
All Exons
Exon 1.5b (A:132-160 | B:0-160)
Exon 1.6 (A:160-217 | B:160-217)
Exon 1.7 (A:218-232 | B:218-232)
Exon 1.8 (A:233-239 | B:233-239)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4/1.5b
2: Boundary 1.5b/1.6
3: Boundary 1.6/1.7
4: Boundary 1.7/1.8
5: Boundary 1.8/1.9
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
ENST00000368644
1
ENSE00002174390
chr10:
131934663-131934776
114
GLRX3_HUMAN
1-31
31
0
-
-
1.2
ENST00000368644
2
ENSE00000728668
chr10:
131943475-131943583
109
GLRX3_HUMAN
31-67
37
0
-
-
1.4
ENST00000368644
4
ENSE00000728671
chr10:
131958259-131958333
75
GLRX3_HUMAN
68-92
25
0
-
-
1.5b
ENST00000368644
5b
ENSE00000728676
chr10:
131959060-131959261
202
GLRX3_HUMAN
93-160
68
2
A:132-160
B:0-160
29
32
1.6
ENST00000368644
6
ENSE00000728678
chr10:
131964771-131964943
173
GLRX3_HUMAN
160-217
58
2
A:160-217
B:160-217
58
58
1.7
ENST00000368644
7
ENSE00000728681
chr10:
131965183-131965244
62
GLRX3_HUMAN
218-238
21
2
A:218-232
B:218-232
15
15
1.8
ENST00000368644
8
ENSE00000728683
chr10:
131967697-131967754
58
GLRX3_HUMAN
238-257
20
2
A:233-239
B:233-239
7
7
1.9
ENST00000368644
9
ENSE00000728687
chr10:
131969848-131969900
53
GLRX3_HUMAN
258-275
18
0
-
-
1.10
ENST00000368644
10
ENSE00000728691
chr10:
131973131-131973170
40
GLRX3_HUMAN
275-288
14
0
-
-
1.11
ENST00000368644
11
ENSE00000577957
chr10:
131973261-131973353
93
GLRX3_HUMAN
289-319
31
0
-
-
1.12a
ENST00000368644
12a
ENSE00001217321
chr10:
131977606-131977684
79
GLRX3_HUMAN
320-335
16
0
-
-
1.13b
ENST00000368644
13b
ENSE00001217252
chr10:
131978377-131978640
264
GLRX3_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3zywa_ (A:)
1b: SCOP_d3zywb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Thioltransferase
(167)
Protein domain
:
automated matches
(27)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d3zywa_
A:
1b
d3zywb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 (51 KB)
Header - Asym.Unit
Biol.Unit 1 (24 KB)
Header - Biol.Unit 1
Biol.Unit 2 (24 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
3ZYW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help