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.
1QWL
Biol. Unit 1
Info
Asym.Unit (192 KB)
Biol.Unit 1 (367 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF HELICOBACTER PYLORI CATALASE
Authors
:
P. C. Loewen, X. Carpena, R. Perez-Luque, C. Rovira, R. Haas, S. Obenbre P. Nicholls, I. Fita
Date
:
02 Sep 03 (Deposition) - 30 Mar 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Beta Barrel, Azide Complex, Oxyferryl Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. C. Loewen, X. Carpena, C. Rovira, A. Ivanich, R. Perez-Luque, R. Haas, S. Obenbreit, P. Nicholls, I. Fita
Structure Of Helicobacter Pylori Catalase, With And Without Formic Acid Bound, At 1. 6 A Resolution
Biochemistry V. 43 3089 2004
[
close entry info
]
Hetero Components
(3, 8)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3a: OXYGEN MOLECULE (OXYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
2
Ligand/Ion
AZIDE ION
2
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
OXY
2
Ligand/Ion
OXYGEN MOLECULE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:47 , ARG A:344 , ARG B:47 , TYR B:345 , HOH B:3091 , HOH B:3103
BINDING SITE FOR RESIDUE AZI B 2600
2
AC2
SOFTWARE
ASP A:46 , ARG A:53 , VAL A:54 , VAL A:55 , HIS A:56 , ARG A:93 , GLY A:112 , PHE A:113 , ALA A:114 , VAL A:127 , GLY A:128 , ASN A:129 , ALA A:139 , PHE A:142 , SER A:198 , HIS A:199 , PHE A:315 , MET A:331 , ARG A:335 , SER A:338 , TYR A:339 , THR A:342 , HIS A:343 , ARG A:346 , OXY A:1600 , HOH A:1606 , HOH A:1629 , HOH A:1667
BINDING SITE FOR RESIDUE HEM A 550
3
AC3
SOFTWARE
LEU B:42 , ASP B:46 , ARG B:53 , VAL B:54 , VAL B:55 , HIS B:56 , ARG B:93 , GLY B:112 , PHE B:113 , ALA B:114 , VAL B:127 , GLY B:128 , ASN B:129 , ALA B:139 , PHE B:142 , GLY B:197 , SER B:198 , HIS B:199 , PHE B:315 , MET B:331 , ARG B:335 , SER B:338 , TYR B:339 , THR B:342 , HIS B:343 , ARG B:346 , HOH B:2603 , HOH B:2609 , HOH B:2657
BINDING SITE FOR RESIDUE HEM B 550
4
AC4
SOFTWARE
HIS A:56 , PHE A:142 , TYR A:339 , HEM A:550 , HOH A:2054
BINDING SITE FOR RESIDUE OXY A 1600
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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:5-489,B:5-489)
2: CATALASE_2 (A:45-61,B:45-61)
3: CATALASE_1 (A:335-343,B:335-343)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CATALASE_3
PS51402
catalase family profile.
CATA_HELPY
5-489
4
A:5-489
B:5-489
2
CATALASE_2
PS00438
Catalase proximal active site signature.
CATA_HELPY
45-61
4
A:45-61
B:45-61
3
CATALASE_1
PS00437
Catalase proximal heme-ligand signature.
CATA_HELPY
335-343
4
A:335-343
B:335-343
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d1qwla_ (A:)
1b: SCOP_d1qwlb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
Catalase I
(32)
Helicobacter pylori [TaxId: 210]
(4)
1a
d1qwla_
A:
1b
d1qwlb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Catalase_rel_1qwlB01 (B:417-484)
1b: PFAM_Catalase_rel_1qwlB02 (B:417-484)
2a: PFAM_Catalase_1qwlB03 (B:9-392)
2b: PFAM_Catalase_1qwlB04 (B:9-392)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Catalase-rel]
(18)
Family
:
Catalase-rel
(18)
Helicobacter pylori (Campylobacter pylori)
(2)
1a
Catalase-rel-1qwlB01
B:417-484
1b
Catalase-rel-1qwlB02
B:417-484
Clan
:
no clan defined [family: Catalase]
(19)
Family
:
Catalase
(19)
Helicobacter pylori (Campylobacter pylori)
(2)
2a
Catalase-1qwlB03
B:9-392
2b
Catalase-1qwlB04
B:9-392
[
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
Asymmetric Unit 2
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 (192 KB)
Header - Asym.Unit
Biol.Unit 1 (367 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
1QWL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
