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.
3V57
Asym. Unit
Info
Asym.Unit (132 KB)
Biol.Unit 1 (184 KB)
Biol.Unit 2 (185 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 B-PHYCOERYTHRIN FROM THE RED ALGAE PORPHYRIDIUM CRUENTUM AT PH8
Authors
:
A. Camara-Artigas
Date
:
16 Dec 11 (Deposition) - 03 Oct 12 (Release) - 03 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (3x)
Biol. Unit 2: C,D (3x)
Keywords
:
Globin-Like, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Camara-Artigas, J. Bacarizo, M. Andujar-Sanchez, E. Ortiz-Salmeron, C. Mesa-Valle, C. Cuadri, J. M. Martin-Garcia, S. Martinez-Rodriguez, T. Mazzuca-Sobczuk, M. J. Ibanez, J. P. Allen
Ph-Dependent Structural Conformations Of B-Phycoerythrin From Porphyridium Cruentum
Febs J. V. 279 3680 2012
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: N-METHYL ASPARAGINE (MENa)
1b: N-METHYL ASPARAGINE (MENb)
2a: PHYCOERYTHROBILIN (PEBa)
2b: PHYCOERYTHROBILIN (PEBb)
2c: PHYCOERYTHROBILIN (PEBc)
2d: PHYCOERYTHROBILIN (PEBd)
2e: PHYCOERYTHROBILIN (PEBe)
2f: PHYCOERYTHROBILIN (PEBf)
2g: PHYCOERYTHROBILIN (PEBg)
2h: PHYCOERYTHROBILIN (PEBh)
2i: PHYCOERYTHROBILIN (PEBi)
2j: PHYCOERYTHROBILIN (PEBj)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MEN
2
Mod. Amino Acid
N-METHYL ASPARAGINE
2
PEB
10
Ligand/Ion
PHYCOERYTHROBILIN
3
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:60 , ALA A:72 , GLY A:73 , LYS A:78 , LYS A:81 , CYS A:82 , ARG A:84 , ASP A:85 , HIS A:88 , TYR A:89 , LEU A:92 , TRP A:108 , TYR A:117 , LEU A:120 , LEU A:122 , ALA A:126 , TYR A:127 , HOH A:247 , HOH A:286 , ILE B:67 , THR B:75 , ASN B:76 , MET B:79 , HOH B:375
BINDING SITE FOR RESIDUE PEB A 201
02
AC2
SOFTWARE
LYS A:43 , ASN A:47 , ALA A:50 , VAL A:51 , GLU A:54 , ARG A:137 , CYS A:139 , ARG A:142 , ASP A:143 , HOH A:168 , HOH A:198 , HOH A:206 , HOH A:385 , THR B:143 , GLY B:156 , ASP B:157 , CYS B:158 , THR B:159 , PEB B:204 , HOH B:211
BINDING SITE FOR RESIDUE PEB A 202
03
AC3
SOFTWARE
LEU A:122 , PRO A:123 , THR A:124 , HOH A:171 , HOH A:437 , PRO C:123 , THR C:124 , HOH C:176 , HOH C:467
BINDING SITE FOR RESIDUE SO4 A 165
04
AC4
SOFTWARE
PRO A:141 , HOH A:389 , LYS B:36 , ASP B:157 , PEB B:204 , HOH B:236
BINDING SITE FOR RESIDUE SO4 A 166
05
AC5
SOFTWARE
MET B:59 , MEN B:72 , CYS B:73 , ARG B:77 , ARG B:78 , ALA B:81 , CYS B:82 , ASP B:85 , ILE B:88 , ARG B:108 , LEU B:113 , LEU B:120 , VAL B:122 , PRO B:123 , SER B:126 , SER B:127 , HOH B:183 , HOH B:284 , HOH B:469
BINDING SITE FOR RESIDUE PEB B 203
06
AC6
SOFTWARE
LEU A:24 , GLU A:25 , GLN A:28 , SO4 A:166 , PEB A:202 , HOH A:389 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , ILE B:142 , ASN B:144 , PHE B:153 , ALA B:154 , ALA B:155 , GLY B:156 , CYS B:158 , HOH B:187 , HOH B:198 , HOH B:235 , HOH B:365 , HOH B:384 , HOH B:391 , ARG C:33 , GLN C:147
BINDING SITE FOR RESIDUE PEB B 204
07
AC7
SOFTWARE
ASN B:47 , CYS B:50 , ASP B:54 , GLY B:58 , CYS B:61 , GLU B:62 , ARG B:129 , ALA B:136 , GLN B:137 , ALA B:146 , THR B:147 , GLU B:148 , ARG B:149 , HOH B:190 , HOH B:199 , HOH B:218 , HOH B:246 , HOH B:425 , HOH B:436
BINDING SITE FOR RESIDUE PEB B 205
08
AC8
SOFTWARE
MET B:1 , ASP B:107 , ARG B:108
BINDING SITE FOR RESIDUE SO4 B 178
09
AC9
SOFTWARE
PHE C:60 , ALA C:72 , GLY C:73 , LYS C:78 , LYS C:81 , CYS C:82 , ARG C:84 , ASP C:85 , HIS C:88 , TYR C:89 , LEU C:92 , TRP C:108 , TYR C:117 , LEU C:120 , LEU C:122 , PRO C:123 , ALA C:126 , TYR C:127 , HOH C:197 , HOH C:203 , HOH C:256 , HOH C:452 , ILE D:67 , THR D:75 , ASN D:76 , MET D:79
BINDING SITE FOR RESIDUE PEB C 206
10
BC1
SOFTWARE
LYS C:43 , ASN C:47 , VAL C:51 , GLU C:54 , ARG C:137 , LEU C:138 , CYS C:139 , ARG C:142 , ASP C:143 , MET C:144 , HOH C:180 , HOH C:216 , HOH C:232 , THR D:147 , GLU D:148 , PEB D:210
BINDING SITE FOR RESIDUE PEB C 207
11
BC2
SOFTWARE
MET D:59 , MEN D:72 , CYS D:73 , ARG D:77 , ARG D:78 , ALA D:81 , CYS D:82 , ARG D:84 , ASP D:85 , ILE D:88 , ARG D:108 , LEU D:120 , VAL D:122 , PRO D:123 , SER D:126 , SER D:127 , HOH D:206 , HOH D:296 , HOH D:358 , HOH D:412 , HOH D:455
BINDING SITE FOR RESIDUE PEB D 208
12
BC3
SOFTWARE
ARG A:33 , GLN A:147 , GLU C:25 , GLN C:28 , ASN D:35 , LYS D:36 , LEU D:38 , ASP D:39 , ILE D:142 , THR D:143 , ASN D:144 , PHE D:153 , ALA D:154 , ALA D:155 , GLY D:156 , CYS D:158 , SO4 D:179 , HOH D:212 , HOH D:233 , HOH D:374 , HOH D:379 , HOH D:410 , HOH D:491
BINDING SITE FOR RESIDUE PEB D 209
13
BC4
SOFTWARE
PEB C:207 , ASN D:47 , CYS D:50 , ASP D:54 , GLY D:58 , CYS D:61 , GLU D:62 , ARG D:129 , ALA D:136 , GLN D:137 , PHE D:141 , ALA D:146 , THR D:147 , GLU D:148 , ARG D:149 , HOH D:182 , HOH D:202 , HOH D:220 , HOH D:262 , HOH D:484
BINDING SITE FOR RESIDUE PEB D 210
14
BC5
SOFTWARE
MET D:1 , ARG D:108 , HOH D:461
BINDING SITE FOR RESIDUE SO4 D 178
15
BC6
SOFTWARE
LYS D:36 , GLY D:156 , ASP D:157 , PEB D:209 , HOH D:448
BINDING SITE FOR RESIDUE SO4 D 179
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3v57a_ (A:)
1b: SCOP_d3v57b_ (B:)
1c: SCOP_d3v57c_ (C:)
1d: SCOP_d3v57d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Globin-like
(1351)
Superfamily
:
Globin-like
(1308)
Family
:
Phycocyanin-like phycobilisome proteins
(65)
Protein domain
:
automated matches
(19)
Red alga (Porphyridium purpureum) [TaxId: 35688]
(2)
1a
d3v57a_
A:
1b
d3v57b_
B:
1c
d3v57c_
C:
1d
d3v57d_
D:
[
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
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 (132 KB)
Header - Asym.Unit
Biol.Unit 1 (184 KB)
Header - Biol.Unit 1
Biol.Unit 2 (185 KB)
Header - Biol.Unit 2
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
3V57
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help