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.
3C2W
Asym. Unit
Info
Asym.Unit (1.3 MB)
Biol.Unit 1 (332 KB)
Biol.Unit 2 (337 KB)
Biol.Unit 3 (338 KB)
Biol.Unit 4 (333 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 THE PHOTOSENSORY CORE DOMAIN OF P. AERUGINOSA BACTERIOPHYTOCHROME PABPHP IN THE PFR STATE
Authors
:
X. Yang, J. Kuk, K. Moffat
Date
:
25 Jan 08 (Deposition) - 23 Sep 08 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: E,F (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: G,H (1x)
Biol. Unit 4: A,B (1x)
Keywords
:
Knot Structure, Chromophore, Kinase, Phosphoprotein, Photoreceptor Protein, Receptor, Sensory Transduction, Transferase, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Yang, J. Kuk, K. Moffat
Crystal Structure Of Pseudomonas Aeruginosa Bacteriophytochrome: Photoconversion And Signal Transduction.
Proc. Natl. Acad. Sci. Usa V. 105 14715 2008
[
close entry info
]
Hetero Components
(1, 8)
Info
All Hetero Components
1a: BILIVERDINE IX ALPHA (BLAa)
1b: BILIVERDINE IX ALPHA (BLAb)
1c: BILIVERDINE IX ALPHA (BLAc)
1d: BILIVERDINE IX ALPHA (BLAd)
1e: BILIVERDINE IX ALPHA (BLAe)
1f: BILIVERDINE IX ALPHA (BLAf)
1g: BILIVERDINE IX ALPHA (BLAg)
1h: BILIVERDINE IX ALPHA (BLAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BLA
8
Ligand/Ion
BILIVERDINE IX ALPHA
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:12 , GLU A:13 , TYR A:163 , GLN A:188 , TYR A:190 , SER A:193 , ASP A:194 , ILE A:195 , PRO A:196 , TYR A:203 , ARG A:209 , HIS A:247 , TYR A:250 , SER A:275 , HIS A:277 , HOH A:901 , HOH A:905
BINDING SITE FOR RESIDUE BLA A 900
2
AC2
SOFTWARE
CYS B:12 , TYR B:163 , GLN B:188 , TYR B:190 , ASP B:194 , PRO B:196 , TYR B:203 , ARG B:209 , SER B:244 , HIS B:247 , TYR B:250 , SER B:259 , SER B:275 , HIS B:277
BINDING SITE FOR RESIDUE BLA B 900
3
AC3
SOFTWARE
CYS C:12 , ILE C:17 , TYR C:163 , GLN C:188 , TYR C:190 , SER C:193 , ASP C:194 , PRO C:196 , TYR C:203 , ARG C:209 , HIS C:247 , TYR C:250 , SER C:275 , HIS C:277 , ARG C:453 , HOH C:901
BINDING SITE FOR RESIDUE BLA C 900
4
AC4
SOFTWARE
CYS D:12 , GLU D:13 , TYR D:163 , GLN D:188 , TYR D:190 , ASP D:194 , TYR D:203 , ARG D:209 , SER D:244 , ILE D:246 , HIS D:247 , TYR D:250 , SER D:275 , HIS D:277 , HOH D:902
BINDING SITE FOR RESIDUE BLA D 900
5
AC5
SOFTWARE
CYS E:12 , TYR E:163 , TYR E:185 , TYR E:190 , ASP E:194 , PRO E:196 , TYR E:203 , ARG E:209 , SER E:244 , HIS E:247 , TYR E:250 , SER E:275 , HIS E:277
BINDING SITE FOR RESIDUE BLA E 900
6
AC6
SOFTWARE
CYS F:12 , TYR F:163 , GLN F:188 , ASP F:194 , PRO F:196 , TYR F:203 , ARG F:209 , ARG F:241 , SER F:244 , HIS F:247 , TYR F:250 , SER F:275 , HOH F:901
BINDING SITE FOR RESIDUE BLA F 900
7
AC7
SOFTWARE
CYS G:12 , TYR G:163 , TYR G:185 , GLN G:188 , TYR G:190 , ASP G:194 , ILE G:195 , PRO G:196 , TYR G:203 , ARG G:209 , ILE G:211 , HIS G:247 , TYR G:250 , SER G:275 , HIS G:277 , HOH G:901 , HOH G:905
BINDING SITE FOR RESIDUE BLA G 900
8
AC8
SOFTWARE
CYS H:12 , TYR H:163 , GLN H:188 , TYR H:190 , ASP H:194 , TYR H:203 , ARG H:209 , ARG H:241 , SER H:244 , TYR H:250 , SER H:275 , HIS H:277 , HOH H:902
BINDING SITE FOR RESIDUE BLA H 900
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: PHYTOCHROME_2 (A:139-297,B:139-297,C:139-297,D:13...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PHYTOCHROME_2
PS50046
Phytochrome chromophore attachment site domain profile.
BPHY_PSEAE
139-297
8
A:139-297
B:139-297
C:139-297
D:139-297
E:139-297
F:139-297
G:139-297
H:139-297
[
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
(3, 24)
Info
All SCOP Domains
1a: SCOP_d3c2wa1 (A:118-309)
1b: SCOP_d3c2wb1 (B:118-309)
1c: SCOP_d3c2wc1 (C:118-309)
1d: SCOP_d3c2wd1 (D:118-309)
1e: SCOP_d3c2we1 (E:118-309)
1f: SCOP_d3c2wf1 (F:118-309)
1g: SCOP_d3c2wg1 (G:118-309)
1h: SCOP_d3c2wh1 (H:118-309)
2a: SCOP_d3c2wa2 (A:310-494)
2b: SCOP_d3c2wb2 (B:310-497)
2c: SCOP_d3c2wc2 (C:310-496)
2d: SCOP_d3c2wd2 (D:310-496)
2e: SCOP_d3c2we2 (E:310-495)
2f: SCOP_d3c2wf2 (F:310-498)
2g: SCOP_d3c2wg2 (G:310-497)
2h: SCOP_d3c2wh2 (H:310-496)
3a: SCOP_d3c2wa3 (A:5-117)
3b: SCOP_d3c2wb3 (B:5-117)
3c: SCOP_d3c2wc3 (C:5-117)
3d: SCOP_d3c2wd3 (D:5-117)
3e: SCOP_d3c2we3 (E:5-115)
3f: SCOP_d3c2wf3 (F:5-117)
3g: SCOP_d3c2wg3 (G:5-117)
3h: SCOP_d3c2wh3 (H:5-117)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Profilin-like
(304)
Superfamily
:
GAF domain-like
(54)
Family
:
GAF domain
(24)
Protein domain
:
Bacteriophytochrome BphP
(8)
Pseudomonas aeruginosa [TaxId: 287]
(5)
1a
d3c2wa1
A:118-309
1b
d3c2wb1
B:118-309
1c
d3c2wc1
C:118-309
1d
d3c2wd1
D:118-309
1e
d3c2we1
E:118-309
1f
d3c2wf1
F:118-309
1g
d3c2wg1
G:118-309
1h
d3c2wh1
H:118-309
Family
:
Phytochrome-specific domain
(5)
Protein domain
:
Bacteriophytochrome BphP
(4)
Pseudomonas aeruginosa [TaxId: 287]
(4)
2a
d3c2wa2
A:310-494
2b
d3c2wb2
B:310-497
2c
d3c2wc2
C:310-496
2d
d3c2wd2
D:310-496
2e
d3c2we2
E:310-495
2f
d3c2wf2
F:310-498
2g
d3c2wg2
G:310-497
2h
d3c2wh2
H:310-496
Superfamily
:
PYP-like sensor domain (PAS domain)
(163)
Family
:
BphP N-terminal domain-like
(12)
Protein domain
:
Bacteriophytochrome BphP
(10)
Pseudomonas aeruginosa [TaxId: 287]
(7)
3a
d3c2wa3
A:5-117
3b
d3c2wb3
B:5-117
3c
d3c2wc3
C:5-117
3d
d3c2wd3
D:5-117
3e
d3c2we3
E:5-115
3f
d3c2wf3
F:5-117
3g
d3c2wg3
G:5-117
3h
d3c2wh3
H:5-117
[
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
Chain E
Chain F
Chain G
Chain H
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 (1.3 MB)
Header - Asym.Unit
Biol.Unit 1 (332 KB)
Header - Biol.Unit 1
Biol.Unit 2 (337 KB)
Header - Biol.Unit 2
Biol.Unit 3 (338 KB)
Header - Biol.Unit 3
Biol.Unit 4 (333 KB)
Header - Biol.Unit 4
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
3C2W
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help