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.
1UBB
Asym. Unit
Info
Asym.Unit (44 KB)
Biol.Unit 1 (40 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 RAT HO-1 IN COMPLEX WITH FERROUS HEME
Authors
:
M. Sugishima, H. Sakamoto, Y. Higashimoto, M. Noguchi, K. Fukuyama
Date
:
03 Apr 03 (Deposition) - 02 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Oxidoreductase, Microsome, Multigene Family
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukuyama
Crystal Structures Of Ferrous And Co-, Cn(-)-, And No-Bound Forms Of Rat Heme Oxygenase-1 (Ho-1) In Complex With Heme: Structural Implications For Discrimination Between Co And O(2) In Ho-1.
Biochemistry V. 42 9898 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:18 , HIS A:25 , GLU A:29 , MET A:34 , TYR A:134 , THR A:135 , ARG A:136 , GLY A:139 , SER A:142 , GLY A:143 , LEU A:147 , LYS A:179 , ARG A:183 , PHE A:207 , ASN A:210 , HOH A:338 , HOH A:344
BINDING SITE FOR RESIDUE HEM A 300
[
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, 1)
Info
All PROSITE Patterns/Profiles
1: HEME_OXYGENASE (A:129-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HEME_OXYGENASE
PS00593
Heme oxygenase signature.
HMOX1_RAT
129-139
1
A:129-139
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.2 (A:11-48)
Exon 1.3b (A:49-212)
Exon 1.4 (A:213-222)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3b
3: Boundary 1.3b/1.4
4: Boundary 1.4/1.5a
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
ENSRNOT00000019192
1
ENSRNOE00000437660
chr19:
13963139-13963277
139
HMOX1_RAT
1-8
8
0
-
-
1.2
ENSRNOT00000019192
2
ENSRNOE00000433615
chr19:
13965179-13965299
121
HMOX1_RAT
8-48
41
1
A:11-48
38
1.3b
ENSRNOT00000019192
3b
ENSRNOE00000135098
chr19:
13966126-13966617
492
HMOX1_RAT
49-212
164
1
A:49-212
164
1.4
ENSRNOT00000019192
4
ENSRNOE00000135373
chr19:
13968127-13968226
100
HMOX1_RAT
213-246
34
1
A:213-222
10
1.5a
ENSRNOT00000019192
5a
ENSRNOE00000265745
chr19:
13969266-13969955
690
HMOX1_RAT
246-289
44
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1ubba_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Heme oxygenase-like
(107)
Superfamily
:
Heme oxygenase-like
(107)
Family
:
Eukaryotic type heme oxygenase
(69)
Protein domain
:
Heme oxygenase-1 (HO-1)
(49)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(25)
1a
d1ubba_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1ubbA00 (A:11-222)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Heme Oxygenase; Chain A
(84)
Homologous Superfamily
:
Heme Oxygenase; Chain A
(84)
Norway rat (Rattus norvegicus)
(13)
1a
1ubbA00
A:11-222
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Heme_oxygenase_1ubbA01 (A:11-216)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HO
(49)
Family
:
Heme_oxygenase
(37)
Rattus norvegicus (Rat)
(4)
1a
Heme_oxygenase-1ubbA01
A:11-216
[
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
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 (44 KB)
Header - Asym.Unit
Biol.Unit 1 (40 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
1UBB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
