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.
1GJQ
Asym. Unit
Info
Asym.Unit (194 KB)
Biol.Unit 1 (187 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PSEUDOMONAS AERUGINOSA CD1 NITRITE REDUCTASE REDUCED CYANIDE COMPLEX
Authors
:
D. Nurizzo, K. Brown, M. Tegoni, C. Cambillau
Date
:
01 Aug 01 (Deposition) - 01 Aug 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Reductase, Oxidoreductase, Electron Transport, Heme
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Sun, M. Arese, M. Brunori, D. Nurizzo, K. Brown, C. Cambillau, M. Tegoni, F. Cutruzzola
Cyanide Binding To Cd(1) Nitrite Reductase From Pseudomonas Aeruginosa: Role Of The Active-Site His369 In Ligand Stabilization.
Biochem. Biophys. Res. Commun. V. 291 1 2002
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: CYANIDE ION (CYNa)
1b: CYANIDE ION (CYNb)
2a: HEME D (DHEa)
2b: HEME D (DHEb)
3a: HEME C (HECa)
3b: HEME C (HECb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CYN
2
Ligand/Ion
CYANIDE ION
2
DHE
2
Ligand/Ion
HEME D
3
HEC
2
Ligand/Ion
HEME C
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:327 , HIS A:369 , DHE A:602 , TYR B:10
BINDING SITE FOR RESIDUE CYN A 603
2
AC2
SOFTWARE
TYR A:10 , HIS B:327 , HIS B:369 , DHE B:602
BINDING SITE FOR RESIDUE CYN B 603
3
AC3
SOFTWARE
ARG A:46 , CYS A:47 , CYS A:50 , HIS A:51 , THR A:59 , GLY A:60 , LYS A:61 , LEU A:63 , ARG A:71 , LEU A:79 , THR A:84 , LEU A:86 , GLY A:87 , MET A:88 , TRP A:91
BINDING SITE FOR RESIDUE HEC A 601
4
AC4
SOFTWARE
ARG A:156 , HIS A:182 , ARG A:185 , ARG A:198 , ARG A:225 , SER A:226 , TYR A:245 , ALA A:284 , ILE A:285 , HIS A:327 , ARG A:372 , PHE A:425 , PHE A:441 , GLN A:483 , GLY A:531 , PHE A:533 , CYN A:603 , HOH A:2103 , HOH A:2107 , HOH A:2124 , HOH A:2185 , HOH A:2209 , HOH A:2282 , HOH A:2283 , HOH A:2284 , HOH A:2285 , TYR B:10 , HOH B:2009
BINDING SITE FOR RESIDUE DHE A 602
5
AC5
SOFTWARE
ARG B:46 , CYS B:47 , CYS B:50 , HIS B:51 , THR B:59 , GLY B:60 , LYS B:61 , LEU B:63 , ARG B:71 , LEU B:79 , THR B:84 , LEU B:86 , GLY B:87 , MET B:88 , TRP B:91 , HOH B:2308
BINDING SITE FOR RESIDUE HEC B 601
6
AC6
SOFTWARE
TYR A:10 , ALA A:13 , ARG B:156 , HIS B:182 , ILE B:183 , ARG B:185 , ARG B:198 , ARG B:225 , SER B:226 , TYR B:245 , ALA B:284 , ILE B:285 , HIS B:327 , ARG B:372 , PHE B:425 , PHE B:441 , GLN B:483 , GLY B:531 , PHE B:533 , CYN B:603 , HOH B:2120 , HOH B:2122 , HOH B:2124 , HOH B:2310 , HOH B:2311 , HOH B:2312 , HOH B:2313 , HOH B:2314
BINDING SITE FOR RESIDUE DHE B 602
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: CYTC (A:34-113,B:34-113)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CYTC
PS51007
Cytochrome c family profile.
NIRS_PSEAE
59-138
2
A:34-113
B:34-113
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1gjqa1 (A:3-117)
1b: SCOP_d1gjqb1 (B:5-117)
2a: SCOP_d1gjqa2 (A:118-543)
2b: SCOP_d1gjqb2 (B:118-543)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
N-terminal (heme c) domain of cytochrome cd1-nitrite reductase
(22)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1gjqa1
A:3-117
1b
d1gjqb1
B:5-117
Class
:
All beta proteins
(24004)
Fold
:
8-bladed beta-propeller
(135)
Superfamily
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Family
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Protein domain
:
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
(22)
Pseudomonas aeruginosa [TaxId: 287]
(9)
2a
d1gjqa2
A:118-543
2b
d1gjqb2
B:118-543
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1gjqA01 (A:6-116)
1b: CATH_1gjqB01 (B:6-116)
2a: CATH_1gjqA02 (A:117-543)
2b: CATH_1gjqB02 (B:117-543)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Pseudomonas aeruginosa. Organism_taxid: 287
(4)
1a
1gjqA01
A:6-116
1b
1gjqB01
B:6-116
Class
:
Mainly Beta
(13760)
Architecture
:
8 Propellor
(110)
Topology
:
Methanol Dehydrogenase; Chain A
(110)
Homologous Superfamily
:
[code=2.140.10.20, no name defined]
(22)
Pseudomonas aeruginosa. Organism_taxid: 287
(1)
2a
1gjqA02
A:117-543
2b
1gjqB02
B:117-543
[
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
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 (194 KB)
Header - Asym.Unit
Biol.Unit 1 (187 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
1GJQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
