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.
1YEP
Asym. Unit
Info
Asym.Unit (145 KB)
Biol.Unit 1 (278 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURAL AND BIOCHEMICAL ANALYSIS OF THE LINK BETWEEN ENZYMATIC ACTIVITY AND OLGOMERIZATION IN AHPC, A BACTERIAL PEROXIREDOXIN.
Authors
:
D. Parsonage, D. S. Youngblood, G. N. Sarma, Z. A. Wood, P. A. Karplus, L.
Date
:
28 Dec 04 (Deposition) - 16 Aug 05 (Release) - 09 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (2x)
Keywords
:
Ahpc, Peroxiredoxin, Peroxidase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Parsonage, D. S. Youngblood, G. N. Sarma, Z. A. Wood, P. A. Karplus, L. B. Poole
Analysis Of The Link Between Enzymatic Activity And Oligomeric State In Ahpc, A Bacterial Peroxiredoxin.
Biochemistry V. 44 10583 2005
[
close entry info
]
Hetero Components
(1, 9)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
9
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
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
TYR A:38 , VAL A:45 , CYS A:46 , PRO A:47 , LEU A:50 , ARG A:119 , HOH A:1064 , HOH A:1066
BINDING SITE FOR RESIDUE SO4 A 801
2
AC2
SOFTWARE
TYR B:38 , VAL B:45 , PRO B:47 , ARG B:119 , HOH B:2066
BINDING SITE FOR RESIDUE SO4 B 802
3
AC3
SOFTWARE
TYR C:38 , VAL C:45 , PRO C:47 , GLU C:49 , ARG C:119
BINDING SITE FOR RESIDUE SO4 C 803
4
AC4
SOFTWARE
CYS D:46 , GLU D:49 , LEU D:50 , ARG D:142
BINDING SITE FOR RESIDUE SO4 D 804
5
AC5
SOFTWARE
TYR E:38 , VAL E:45 , ARG E:119
BINDING SITE FOR RESIDUE SO4 E 805
6
AC6
SOFTWARE
SER A:85 , GLU A:86 , THR A:87
BINDING SITE FOR RESIDUE SO4 A 811
7
AC7
SOFTWARE
LYS A:168 , PRO B:47 , SER B:85 , GLU B:86 , THR B:87
BINDING SITE FOR RESIDUE SO4 B 812
8
AC8
SOFTWARE
PRO C:47 , SER C:85 , GLU C:86 , THR C:87
BINDING SITE FOR RESIDUE SO4 C 813
9
AC9
SOFTWARE
SER D:85 , GLU D:86 , THR D:87
BINDING SITE FOR RESIDUE SO4 D 814
[
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, 5)
Info
All PROSITE Patterns/Profiles
1: THIOREDOXIN_2 (A:1-156,B:1-156,C:1-156,D:1-156,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_2
PS51352
Thioredoxin domain profile.
AHPC_SALTY
2-157
5
A:1-156
B:1-156
C:1-156
D:1-156
E:1-156
[
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.
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1yepa_ (A:)
1b: SCOP_d1yepb_ (B:)
1c: SCOP_d1yepc_ (C:)
1d: SCOP_d1yepd_ (D:)
1e: SCOP_d1yepe_ (E:)
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
:
Glutathione peroxidase-like
(136)
Protein domain
:
Alkyl hydroperoxide reductase AhpC
(9)
Salmonella typhimurium [TaxId: 90371]
(5)
1a
d1yepa_
A:
1b
d1yepb_
B:
1c
d1yepc_
C:
1d
d1yepd_
D:
1e
d1yepe_
E:
[
close SCOP info
]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1yepC00 (C:1-163)
1b: CATH_1yepB00 (B:1-165)
1c: CATH_1yepE00 (E:1-165)
1d: CATH_1yepD00 (D:1-166)
1e: CATH_1yepA00 (A:1-168)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Salmonella typhimurium. Organism_taxid: 602.
(6)
1a
1yepC00
C:1-163
1b
1yepB00
B:1-165
1c
1yepE00
E:1-165
1d
1yepD00
D:1-166
1e
1yepA00
A:1-168
[
close CATH info
]
Pfam Domains
(2, 10)
Info
all PFAM domains
1a: PFAM_AhpC_TSA_1yepE01 (E:3-133)
1b: PFAM_AhpC_TSA_1yepE02 (E:3-133)
1c: PFAM_AhpC_TSA_1yepE03 (E:3-133)
1d: PFAM_AhpC_TSA_1yepE04 (E:3-133)
1e: PFAM_AhpC_TSA_1yepE05 (E:3-133)
2a: PFAM_1_cysPrx_C_1yepE06 (E:153-165)
2b: PFAM_1_cysPrx_C_1yepE07 (E:153-165)
2c: PFAM_1_cysPrx_C_1yepE08 (E:153-165)
2d: PFAM_1_cysPrx_C_1yepE09 (E:153-165)
2e: PFAM_1_cysPrx_C_1yepE10 (E:153-165)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Thioredoxin
(367)
Family
:
AhpC-TSA
(28)
Salmonella typhimurium
(5)
1a
AhpC-TSA-1yepE01
E:3-133
1b
AhpC-TSA-1yepE02
E:3-133
1c
AhpC-TSA-1yepE03
E:3-133
1d
AhpC-TSA-1yepE04
E:3-133
1e
AhpC-TSA-1yepE05
E:3-133
Clan
:
no clan defined [family: 1-cysPrx_C]
(19)
Family
:
1-cysPrx_C
(19)
Salmonella typhimurium
(5)
2a
1-cysPrx_C-1yepE06
E:153-165
2b
1-cysPrx_C-1yepE07
E:153-165
2c
1-cysPrx_C-1yepE08
E:153-165
2d
1-cysPrx_C-1yepE09
E:153-165
2e
1-cysPrx_C-1yepE10
E:153-165
[
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
Chain C
Chain D
Chain E
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 (145 KB)
Header - Asym.Unit
Biol.Unit 1 (278 KB)
Header - Biol.Unit 1
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
1YEP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
