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.
3PQ6
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF I274C VARIANT OF E. COLI KATE[] - IMAGES 25-30
Authors
:
P. C. Loewen, V. Jha, S. Louis, P. Chelikani, X. Carpena, I. Fita
Date
:
25 Nov 10 (Deposition) - 22 Dec 10 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Catalase, I274C Variant, Heme Orientation, X-Ray Damage, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Jha, S. Louis, P. Chelikani, X. Carpena, L. J. Donald, I. Fita, P. C. Loewen
Modulation Of Heme Orientation And Binding By A Single Residue In Catalase Hpii Of Escherichia Coli.
Biochemistry V. 50 2101 2011
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: HYDROSULFURIC ACID (H2Sa)
1b: HYDROSULFURIC ACID (H2Sb)
1c: HYDROSULFURIC ACID (H2Sc)
1d: HYDROSULFURIC ACID (H2Sd)
2a: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDDa)
2b: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDDb)
2c: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDDc)
2d: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDDd)
3a: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDEa)
3b: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDEb)
3c: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDEc)
3d: CIS-HEME D HYDROXYCHLORIN GAMMA-SP... (HDEd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
H2S
4
Ligand/Ion
HYDROSULFURIC ACID
2
HDD
4
Ligand/Ion
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
3
HDE
4
Ligand/Ion
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:125 , VAL A:127 , HIS A:128 , ARG A:165 , GLY A:184 , ALA A:186 , VAL A:199 , GLY A:200 , ASN A:201 , PHE A:206 , PHE A:214 , CYS A:274 , HIS A:275 , PHE A:391 , LEU A:407 , ARG A:411 , SER A:414 , TYR A:415 , THR A:418 , GLN A:419 , H2S A:754 , HOH A:792 , HOH A:849 , HOH A:881 , HOH A:3592
BINDING SITE FOR RESIDUE HDD A 760
02
AC2
SOFTWARE
ARG B:125 , VAL B:127 , HIS B:128 , ARG B:165 , GLY B:184 , VAL B:199 , GLY B:200 , ASN B:201 , PHE B:206 , PHE B:214 , CYS B:274 , PHE B:391 , LEU B:407 , ARG B:411 , SER B:414 , TYR B:415 , THR B:418 , GLN B:419 , ARG B:422 , H2S B:754 , HOH B:848 , HOH B:898 , HOH B:927 , HOH B:3593
BINDING SITE FOR RESIDUE HDD B 760
03
AC3
SOFTWARE
ARG C:125 , VAL C:127 , HIS C:128 , ARG C:165 , GLY C:184 , VAL C:199 , GLY C:200 , ASN C:201 , PHE C:206 , PHE C:214 , CYS C:274 , PHE C:391 , LEU C:407 , ARG C:411 , SER C:414 , TYR C:415 , THR C:418 , GLN C:419 , ARG C:422 , H2S C:754 , HOH C:871 , HOH C:929 , HOH C:964 , HOH C:3277
BINDING SITE FOR RESIDUE HDD C 760
04
AC4
SOFTWARE
ARG D:125 , VAL D:127 , HIS D:128 , ARG D:165 , GLY D:184 , VAL D:199 , GLY D:200 , ASN D:201 , PHE D:214 , CYS D:274 , HIS D:275 , PHE D:391 , LEU D:407 , ARG D:411 , SER D:414 , TYR D:415 , THR D:418 , GLN D:419 , ARG D:422 , H2S D:754 , HOH D:1295 , HOH D:1353 , HOH D:1388 , HOH D:3252
BINDING SITE FOR RESIDUE HDD D 760
05
AC5
SOFTWARE
ARG A:125 , VAL A:127 , HIS A:128 , ARG A:165 , VAL A:199 , GLY A:200 , ASN A:201 , ALA A:211 , PHE A:214 , CYS A:274 , PHE A:391 , LEU A:407 , ARG A:411 , SER A:414 , TYR A:415 , THR A:418 , GLN A:419 , ARG A:422 , H2S A:754 , HOH A:792 , HOH A:849 , HOH A:1082 , HOH A:3592
BINDING SITE FOR RESIDUE HDE A 761
06
AC6
SOFTWARE
ARG B:125 , VAL B:127 , HIS B:128 , ARG B:165 , GLY B:184 , VAL B:199 , GLY B:200 , ASN B:201 , ALA B:211 , PHE B:214 , CYS B:274 , HIS B:275 , PHE B:391 , LEU B:407 , ARG B:411 , SER B:414 , TYR B:415 , THR B:418 , GLN B:419 , H2S B:754 , HOH B:848 , HOH B:898 , HOH B:3593
BINDING SITE FOR RESIDUE HDE B 761
07
AC7
SOFTWARE
ARG C:125 , VAL C:127 , HIS C:128 , ARG C:165 , VAL C:199 , GLY C:200 , ASN C:201 , ALA C:211 , PHE C:214 , CYS C:274 , HIS C:275 , PHE C:391 , LEU C:407 , ARG C:411 , SER C:414 , TYR C:415 , GLN C:419 , H2S C:754 , HOH C:871 , HOH C:929 , HOH C:1263 , HOH C:3277
BINDING SITE FOR RESIDUE HDE C 761
08
AC8
SOFTWARE
ARG D:125 , VAL D:127 , HIS D:128 , ARG D:165 , GLY D:184 , VAL D:199 , GLY D:200 , ASN D:201 , ALA D:211 , PHE D:214 , CYS D:274 , PHE D:391 , LEU D:407 , ARG D:411 , SER D:414 , TYR D:415 , THR D:418 , GLN D:419 , H2S D:754 , HOH D:1295 , HOH D:1353 , HOH D:3252
BINDING SITE FOR RESIDUE HDE D 761
09
AC9
SOFTWARE
CYS A:274 , HDD A:760 , HDE A:761 , HOH A:3466
BINDING SITE FOR RESIDUE H2S A 754
10
BC1
SOFTWARE
CYS B:274 , HDD B:760 , HDE B:761
BINDING SITE FOR RESIDUE H2S B 754
11
BC2
SOFTWARE
CYS C:274 , HDD C:760 , HDE C:761
BINDING SITE FOR RESIDUE H2S C 754
12
BC3
SOFTWARE
CYS D:274 , HDD D:760 , HDE D:761 , HOH D:2756
BINDING SITE FOR RESIDUE H2S D 754
[
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
(3, 12)
Info
All PROSITE Patterns/Profiles
1: CATALASE_3 (A:77-568,B:77-568,C:77-568,D:77-56...)
2: CATALASE_2 (A:117-133,B:117-133,C:117-133,D:11...)
3: CATALASE_1 (A:411-419,B:411-419,C:411-419,D:41...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CATALASE_3
PS51402
catalase family profile.
CATE_ECOLI
77-568
4
A:77-568
B:77-568
C:77-568
D:77-568
2
CATALASE_2
PS00438
Catalase proximal active site signature.
CATE_ECOLI
117-133
4
A:117-133
B:117-133
C:117-133
D:117-133
3
CATALASE_1
PS00437
Catalase proximal heme-ligand signature.
CATE_ECOLI
411-419
4
A:411-419
B:411-419
C:411-419
D:411-419
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3pq6a2 (A:598-753)
1b: SCOP_d3pq6b2 (B:598-753)
1c: SCOP_d3pq6c2 (C:598-753)
1d: SCOP_d3pq6d2 (D:598-753)
2a: SCOP_d3pq6a1 (A:28-597)
2b: SCOP_d3pq6b1 (B:28-597)
2c: SCOP_d3pq6c1 (C:28-597)
2d: SCOP_d3pq6d1 (D:28-597)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Class I glutamine amidotransferase-like
(173)
Family
:
automated matches
(40)
Protein domain
:
automated matches
(40)
Escherichia coli K-12 [TaxId: 83333]
(19)
1a
d3pq6a2
A:598-753
1b
d3pq6b2
B:598-753
1c
d3pq6c2
C:598-753
1d
d3pq6d2
D:598-753
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Heme-dependent catalase-like
(82)
Superfamily
:
Heme-dependent catalase-like
(82)
Family
:
Heme-dependent catalases
(80)
Protein domain
:
automated matches
(32)
Escherichia coli K-12 [TaxId: 83333]
(19)
2a
d3pq6a1
A:28-597
2b
d3pq6b1
B:28-597
2c
d3pq6c1
C:28-597
2d
d3pq6d1
D:28-597
[
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
Chain C
Chain D
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 (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (1.0 MB)
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
3PQ6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
