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.
1QWM
Biol. Unit 1
Info
Asym.Unit (194 KB)
Biol.Unit 1 (368 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 WITH FORMIC ACID BOUND
Authors
:
P. C. Loewen, X. Carpena, R. Perez-Luque, C. Rovira, R. Haas, S. Odenbre 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, Formate Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. C. Loewen, X. Carpena, C. Rovira, A. Ivancich, 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, 78)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
2a: FORMIC ACID (FMTa)
2aa: FORMIC ACID (FMTaa)
2ab: FORMIC ACID (FMTab)
2ac: FORMIC ACID (FMTac)
2ad: FORMIC ACID (FMTad)
2ae: FORMIC ACID (FMTae)
2af: FORMIC ACID (FMTaf)
2ag: FORMIC ACID (FMTag)
2ah: FORMIC ACID (FMTah)
2ai: FORMIC ACID (FMTai)
2aj: FORMIC ACID (FMTaj)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
2f: FORMIC ACID (FMTf)
2g: FORMIC ACID (FMTg)
2h: FORMIC ACID (FMTh)
2i: FORMIC ACID (FMTi)
2j: FORMIC ACID (FMTj)
2k: FORMIC ACID (FMTk)
2l: FORMIC ACID (FMTl)
2m: FORMIC ACID (FMTm)
2n: FORMIC ACID (FMTn)
2o: FORMIC ACID (FMTo)
2p: FORMIC ACID (FMTp)
2q: FORMIC ACID (FMTq)
2r: FORMIC ACID (FMTr)
2s: FORMIC ACID (FMTs)
2t: FORMIC ACID (FMTt)
2u: FORMIC ACID (FMTu)
2v: FORMIC ACID (FMTv)
2w: FORMIC ACID (FMTw)
2x: FORMIC ACID (FMTx)
2y: FORMIC ACID (FMTy)
2z: FORMIC ACID (FMTz)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
2
Ligand/Ion
AZIDE ION
2
FMT
72
Ligand/Ion
FORMIC ACID
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
[
close Hetero Component info
]
Sites
(39, 39)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:47 , ARG A:344 , FMT A:1713 , FMT A:1735 , ARG B:47 , TYR B:345
BINDING SITE FOR RESIDUE AZI A 2600
02
AC2
SOFTWARE
ASP A:46 , ARG A:53 , VAL A:54 , VAL A:55 , HIS A:56 , ARG A:93 , GLY A:112 , VAL A:127 , GLY A:128 , ASN A:129 , ALA A:139 , PHE A:142 , GLY A:197 , 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 , FMT A:1701 , HOH A:2606 , HOH A:2629 , HOH A:2668
BINDING SITE FOR RESIDUE HEM A 550
03
AC3
SOFTWARE
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 , PHE B:315 , MET B:331 , ARG B:335 , SER B:338 , TYR B:339 , THR B:342 , HIS B:343 , ARG B:346 , FMT B:1702 , HOH B:1739 , HOH B:1745 , HOH B:1792
BINDING SITE FOR RESIDUE HEM B 550
04
AC4
SOFTWARE
HIS A:56 , ASN A:129 , PHE A:134 , PHE A:142 , HEM A:550
BINDING SITE FOR RESIDUE FMT A 1701
05
AC5
SOFTWARE
HIS B:56 , VAL B:97 , ASN B:129 , PHE B:134 , HEM B:550
BINDING SITE FOR RESIDUE FMT B 1702
06
AC6
SOFTWARE
ARG B:108 , ASP B:109 , PRO B:110 , PHE B:135 , GLN B:149 , VAL B:180
BINDING SITE FOR RESIDUE FMT B 1703
07
AC7
SOFTWARE
GLN A:149 , VAL A:163 , TRP A:167 , MET A:181 , HOH A:3041
BINDING SITE FOR RESIDUE FMT A 1704
08
AC8
SOFTWARE
GLN B:149 , PRO B:158 , VAL B:163 , FMT B:1707 , HOH B:1827 , HOH B:2015 , HOH B:2224
BINDING SITE FOR RESIDUE FMT B 1705
09
AC9
SOFTWARE
PRO A:158 , HIS A:160 , HOH A:2784 , HOH A:2855
BINDING SITE FOR RESIDUE FMT A 1706
10
BC1
SOFTWARE
FMT B:1705 , HOH B:1977 , HOH B:2112
BINDING SITE FOR RESIDUE FMT B 1707
11
BC2
SOFTWARE
HIS B:160 , GLU B:450 , SER B:451 , HIS B:454 , HOH B:1817 , HOH B:1986
BINDING SITE FOR RESIDUE FMT B 1708
12
BC3
SOFTWARE
ASP A:183 , ARG A:184 , VAL A:223 , GLU A:440 , HOH A:2717 , HOH A:2732
BINDING SITE FOR RESIDUE FMT A 1709
13
BC4
SOFTWARE
LYS A:58 , ARG A:101 , GLY A:102 , ARG A:151 , ASN A:156 , FMT A:1734 , HOH A:2845 , HOH A:2890
BINDING SITE FOR RESIDUE FMT A 1710
14
BC5
SOFTWARE
LYS A:150 , ARG A:151 , HOH A:2607 , HOH A:2652 , HOH A:3040
BINDING SITE FOR RESIDUE FMT A 1711
15
BC6
SOFTWARE
ALA B:57 , LYS B:58 , GLY B:59 , ARG B:101 , TYR B:306 , GLU B:311 , FMT B:1720 , HOH B:2207
BINDING SITE FOR RESIDUE FMT B 1712
16
BC7
SOFTWARE
ARG A:47 , TYR A:345 , AZI A:2600 , HOH A:2654 , ARG B:344
BINDING SITE FOR RESIDUE FMT A 1713
17
BC8
SOFTWARE
ASN A:130 , TRP A:179 , ARG A:184 , ASP A:194 , HOH A:2694
BINDING SITE FOR RESIDUE FMT A 1714
18
BC9
SOFTWARE
TYR A:371 , TYR B:371
BINDING SITE FOR RESIDUE FMT A 1715
19
CC1
SOFTWARE
PRO A:352 , GLN A:353 , PRO A:359 , PHE A:363 , HOH A:2791 , HOH A:2860 , ALA B:11
BINDING SITE FOR RESIDUE FMT A 1716
20
CC2
SOFTWARE
TYR B:285 , THR B:286 , HOH B:2133
BINDING SITE FOR RESIDUE FMT B 1717
21
CC3
SOFTWARE
PHE A:247 , ALA A:251 , ASN A:302 , HOH A:2725
BINDING SITE FOR RESIDUE FMT A 1718
22
CC4
SOFTWARE
LYS A:77 , GLY A:323 , SER A:396 , ALA A:397 , ARG A:398
BINDING SITE FOR RESIDUE FMT A 1719
23
CC5
SOFTWARE
LYS B:58 , ARG B:101 , GLY B:102 , ARG B:151 , ASN B:156 , FMT B:1712 , HOH B:2050 , HOH B:2207
BINDING SITE FOR RESIDUE FMT B 1720
24
CC6
SOFTWARE
HOH A:2634 , ARG B:49 , ARG B:101 , HOH B:1801 , HOH B:1916 , HOH B:2050 , HOH B:2085 , HOH B:2177
BINDING SITE FOR RESIDUE FMT B 1721
25
CC7
SOFTWARE
ASP A:194 , HIS A:218 , THR A:219 , HOH A:2928
BINDING SITE FOR RESIDUE FMT A 1722
26
CC8
SOFTWARE
VAL A:223 , LYS A:224 , HOH A:2688 , HOH A:2978
BINDING SITE FOR RESIDUE FMT A 1723
27
CC9
SOFTWARE
LYS A:188 , HOH A:2688 , HOH A:2925
BINDING SITE FOR RESIDUE FMT A 1724
28
DC1
SOFTWARE
LYS A:188 , LEU A:226 , HOH A:2925 , HOH A:2956
BINDING SITE FOR RESIDUE FMT A 1725
29
DC2
SOFTWARE
VAL B:223 , LYS B:224 , HOH B:1830
BINDING SITE FOR RESIDUE FMT B 1726
30
DC3
SOFTWARE
ASP B:183 , HIS B:225 , GLU B:440
BINDING SITE FOR RESIDUE FMT B 1727
31
DC4
SOFTWARE
LYS B:188 , LYS B:224 , HOH B:1830 , HOH B:2143
BINDING SITE FOR RESIDUE FMT B 1728
32
DC5
SOFTWARE
SER B:182 , ASP B:183 , ARG B:184 , TYR B:432 , LEU B:436 , GLU B:440 , HOH B:1897 , HOH B:2000 , HOH B:2225
BINDING SITE FOR RESIDUE FMT B 1729
33
DC6
SOFTWARE
TYR A:371 , FMT A:1735 , PRO B:51 , TYR B:345
BINDING SITE FOR RESIDUE FMT A 1730
34
DC7
SOFTWARE
LEU B:336 , PHE B:337 , ASP B:341 , ARG B:344 , FMT B:1736
BINDING SITE FOR RESIDUE FMT B 1731
35
DC8
SOFTWARE
LEU A:336 , PHE A:337 , ARG A:344 , FMT A:1733
BINDING SITE FOR RESIDUE FMT A 1732
36
DC9
SOFTWARE
ALA A:318 , ARG A:344 , FMT A:1732 , HOH A:2787 , THR B:36 , LEU B:39 , GLU B:40 , HOH B:1800 , HOH B:2160
BINDING SITE FOR RESIDUE FMT A 1733
37
EC1
SOFTWARE
ALA A:57 , LYS A:58 , GLY A:59 , ARG A:101 , TYR A:306 , GLU A:311 , FMT A:1710 , HOH A:2845
BINDING SITE FOR RESIDUE FMT A 1734
38
EC2
SOFTWARE
ARG A:344 , FMT A:1730 , AZI A:2600 , HOH A:2727 , HOH A:2867 , ARG B:47 , TYR B:345
BINDING SITE FOR RESIDUE FMT A 1735
39
EC3
SOFTWARE
THR A:36 , LEU A:39 , GLU A:40 , ALA B:318 , ARG B:344 , FMT B:1731 , HOH B:1917 , HOH B:2011 , HOH B:2179
BINDING SITE FOR RESIDUE FMT B 1736
[
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_d1qwma_ (A:)
1b: SCOP_d1qwmb_ (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
d1qwma_
A:
1b
d1qwmb_
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_1qwmB01 (B:417-484)
1b: PFAM_Catalase_rel_1qwmB02 (B:417-484)
2a: PFAM_Catalase_1qwmB03 (B:9-392)
2b: PFAM_Catalase_1qwmB04 (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-1qwmB01
B:417-484
1b
Catalase-rel-1qwmB02
B:417-484
Clan
:
no clan defined [family: Catalase]
(19)
Family
:
Catalase
(19)
Helicobacter pylori (Campylobacter pylori)
(2)
2a
Catalase-1qwmB03
B:9-392
2b
Catalase-1qwmB04
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 (194 KB)
Header - Asym.Unit
Biol.Unit 1 (368 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
1QWM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help