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.
2VML
Asym. Unit
Info
Asym.Unit (348 KB)
Biol.Unit 1 (333 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE MONOCLINIC STRUCTURE OF PHYCOCYANIN FROM GLOEOBACTER VIOLACEUS
Authors
:
J. W. Murray, S. Benson, J. Barber
Date
:
28 Jan 08 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Photosynthesis, Light-Harvesting, Electron Transport, Transport, Chromophore, Bile Pigment, Phycobilisome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. W. Murray, S. Benson, J. Nield, J. Barber
The Structures Of The Phycobiliproteins Of Gloeobacter Violaceus
To Be Published
[
close entry info
]
Hetero Components
(1, 18)
Info
All Hetero Components
1a: PHYCOCYANOBILIN (CYCa)
1b: PHYCOCYANOBILIN (CYCb)
1c: PHYCOCYANOBILIN (CYCc)
1d: PHYCOCYANOBILIN (CYCd)
1e: PHYCOCYANOBILIN (CYCe)
1f: PHYCOCYANOBILIN (CYCf)
1g: PHYCOCYANOBILIN (CYCg)
1h: PHYCOCYANOBILIN (CYCh)
1i: PHYCOCYANOBILIN (CYCi)
1j: PHYCOCYANOBILIN (CYCj)
1k: PHYCOCYANOBILIN (CYCk)
1l: PHYCOCYANOBILIN (CYCl)
1m: PHYCOCYANOBILIN (CYCm)
1n: PHYCOCYANOBILIN (CYCn)
1o: PHYCOCYANOBILIN (CYCo)
1p: PHYCOCYANOBILIN (CYCp)
1q: PHYCOCYANOBILIN (CYCq)
1r: PHYCOCYANOBILIN (CYCr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CYC
18
Ligand/Ion
PHYCOCYANOBILIN
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:60 , MET A:72 , GLY A:73 , ASN A:78 , LYS A:81 , CYS A:82 , ARG A:84 , ASP A:85 , HIS A:88 , PHE A:92 , TYR A:108 , VAL A:116 , PHE A:120 , LEU A:122 , TRP A:126 , TYR A:127 , HOH A:2055 , HOH A:2056 , HOH A:2057 , HOH A:2058 , HIS F:57 , ILE F:67 , TYR F:74 , PRO F:75 , ASN F:76
BINDING SITE FOR RESIDUE CYC A1082
02
AC2
SOFTWARE
ASN B:72 , ALA B:73 , ARG B:77 , ARG B:78 , ALA B:81 , CYS B:82 , ARG B:84 , ASP B:85 , ILE B:88 , ARG B:108 , LEU B:113 , LEU B:120 , SER B:126 , VAL B:127
BINDING SITE FOR RESIDUE CYC B1082
03
AC3
SOFTWARE
ASN A:21 , LEU A:24 , ASN A:28 , ASN B:35 , LYS B:36 , LEU B:38 , ASP B:39 , VAL B:142 , PRO B:145 , VAL B:148 , THR B:149 , ARG B:150 , GLY B:151 , CYS B:153 , HOH B:2044 , HOH B:2052 , ARG K:33 , GLN K:145
BINDING SITE FOR RESIDUE CYC B1153
04
AC4
SOFTWARE
HIS B:57 , ILE B:67 , TYR B:74 , PRO B:75 , ASN B:76 , HOH B:2026 , TYR C:60 , MET C:72 , GLY C:73 , ASN C:78 , LYS C:81 , CYS C:82 , ARG C:84 , ASP C:85 , HIS C:88 , PHE C:92 , TYR C:108 , VAL C:116 , PHE C:120 , LEU C:122 , TRP C:126 , TYR C:127 , HOH C:2076 , HOH C:2077
BINDING SITE FOR RESIDUE CYC C1082
05
AC5
SOFTWARE
ASN D:72 , ALA 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:113 , LEU D:120 , SER D:126
BINDING SITE FOR RESIDUE CYC D1082
06
AC6
SOFTWARE
ASN C:21 , LEU C:24 , ASN C:28 , ASN D:35 , LYS D:36 , LEU D:38 , ASP D:39 , VAL D:142 , ASN D:143 , PRO D:145 , VAL D:148 , THR D:149 , ARG D:150 , GLY D:151 , CYS D:153 , HOH D:2059 , HOH D:2060 , ARG G:33 , GLN G:145
BINDING SITE FOR RESIDUE CYC D1153
07
AC7
SOFTWARE
HIS D:57 , ILE D:67 , TYR D:74 , PRO D:75 , ASN D:76 , HOH D:2031 , TYR E:60 , MET E:72 , GLY E:73 , ASN E:78 , LYS E:81 , CYS E:82 , ARG E:84 , ASP E:85 , HIS E:88 , PHE E:92 , TYR E:108 , VAL E:116 , PHE E:120 , LEU E:122 , TRP E:126 , TYR E:127 , HOH E:2050 , HOH E:2051
BINDING SITE FOR RESIDUE CYC E1082
08
AC8
SOFTWARE
ASN F:72 , ALA F:73 , ARG F:77 , ARG F:78 , ALA F:81 , CYS F:82 , ARG F:84 , ASP F:85 , ILE F:88 , ARG F:108 , LEU F:113 , LEU F:120 , SER F:126 , VAL F:127 , ALA F:130
BINDING SITE FOR RESIDUE CYC F1082
09
AC9
SOFTWARE
ASN E:21 , LEU E:24 , ASN E:28 , ASN F:35 , LYS F:36 , LEU F:38 , ASP F:39 , VAL F:142 , ASN F:143 , PRO F:145 , VAL F:148 , THR F:149 , ARG F:150 , GLY F:151 , CYS F:153 , HOH F:2061 , HOH F:2062 , ARG I:33 , GLN I:145
BINDING SITE FOR RESIDUE CYC F1153
10
BC1
SOFTWARE
TYR G:60 , MET G:72 , GLY G:73 , ASN G:78 , LYS G:81 , CYS G:82 , ARG G:84 , ASP G:85 , HIS G:88 , PHE G:92 , TYR G:108 , VAL G:116 , PHE G:120 , LEU G:122 , TRP G:126 , TYR G:127 , HOH G:2044 , HOH G:2045 , HOH G:2046 , HIS J:57 , ILE J:67 , TYR J:74 , PRO J:75 , ASN J:76
BINDING SITE FOR RESIDUE CYC G1082
11
BC2
SOFTWARE
ASN H:72 , ALA H:73 , ARG H:77 , ARG H:78 , ALA H:81 , CYS H:82 , ARG H:84 , ASP H:85 , ILE H:88 , ARG H:108 , LEU H:113 , LEU H:120 , SER H:126 , VAL H:127 , ALA H:130
BINDING SITE FOR RESIDUE CYC H1082
12
BC3
SOFTWARE
ARG C:33 , GLN C:145 , ASN G:21 , LEU G:24 , ASN G:28 , ASN H:35 , LYS H:36 , LEU H:38 , ASP H:39 , VAL H:142 , ASN H:143 , PRO H:145 , VAL H:148 , THR H:149 , ARG H:150 , GLY H:151 , CYS H:153 , HOH H:2053 , HOH H:2054 , HOH H:2055 , HOH H:2056
BINDING SITE FOR RESIDUE CYC H1153
13
BC4
SOFTWARE
TYR I:60 , MET I:72 , GLY I:73 , ASN I:78 , LYS I:81 , CYS I:82 , ARG I:84 , ASP I:85 , HIS I:88 , PHE I:92 , TYR I:108 , VAL I:116 , PHE I:120 , LEU I:122 , TRP I:126 , TYR I:127 , HOH I:2047 , HOH I:2070 , HOH I:2071 , HIS L:57 , ILE L:67 , TYR L:74 , PRO L:75 , ASN L:76
BINDING SITE FOR RESIDUE CYC I1082
14
BC5
SOFTWARE
ASN J:72 , ALA J:73 , ARG J:77 , ARG J:78 , ALA J:81 , CYS J:82 , ARG J:84 , ASP J:85 , ILE J:88 , ARG J:108 , LEU J:113 , LEU J:120 , SER J:126 , VAL J:127 , ALA J:130
BINDING SITE FOR RESIDUE CYC J1082
15
BC6
SOFTWARE
ARG E:33 , GLN E:145 , ASN I:21 , LEU I:24 , ASN I:28 , ASN J:35 , LYS J:36 , LEU J:38 , ASP J:39 , VAL J:142 , ASN J:143 , PRO J:145 , VAL J:148 , THR J:149 , ARG J:150 , GLY J:151 , CYS J:153 , HOH J:2072 , HOH J:2073
BINDING SITE FOR RESIDUE CYC J1153
16
BC7
SOFTWARE
HIS H:57 , ILE H:67 , TYR H:74 , PRO H:75 , ASN H:76 , HOH H:2024 , TYR K:60 , MET K:72 , GLY K:73 , ASN K:78 , LYS K:81 , CYS K:82 , ARG K:84 , ASP K:85 , HIS K:88 , PHE K:92 , TYR K:108 , VAL K:116 , PHE K:120 , LEU K:122 , TRP K:126 , TYR K:127 , HOH K:2056 , HOH K:2057
BINDING SITE FOR RESIDUE CYC K1082
17
BC8
SOFTWARE
ASN L:72 , ALA L:73 , ARG L:77 , ARG L:78 , ALA L:81 , CYS L:82 , ARG L:84 , ASP L:85 , ILE L:88 , ARG L:108 , LEU L:113 , LEU L:120 , SER L:126 , VAL L:127 , ALA L:130
BINDING SITE FOR RESIDUE CYC L1082
18
BC9
SOFTWARE
ARG A:33 , GLN A:145 , ASN K:21 , LEU K:24 , ASN K:28 , ASN L:35 , LYS L:36 , LEU L:38 , ASP L:39 , VAL L:142 , ASN L:143 , PRO L:145 , VAL L:148 , THR L:149 , ARG L:150 , GLY L:151 , CYS L:153 , HOH L:2010 , HOH L:2039 , HOH L:2046
BINDING SITE FOR RESIDUE CYC L1153
[
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, 12)
Info
All SCOP Domains
1a: SCOP_d2vmla_ (A:)
1b: SCOP_d2vmlg_ (G:)
1c: SCOP_d2vmlh_ (H:)
1d: SCOP_d2vmli_ (I:)
1e: SCOP_d2vmlj_ (J:)
1f: SCOP_d2vmlk_ (K:)
1g: SCOP_d2vmll_ (L:)
1h: SCOP_d2vmlb_ (B:)
1i: SCOP_d2vmlc_ (C:)
1j: SCOP_d2vmld_ (D:)
1k: SCOP_d2vmle_ (E:)
1l: SCOP_d2vmlf_ (F:)
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)
Gloeobacter violaceus [TaxId: 33072]
(4)
1a
d2vmla_
A:
1b
d2vmlg_
G:
1c
d2vmlh_
H:
1d
d2vmli_
I:
1e
d2vmlj_
J:
1f
d2vmlk_
K:
1g
d2vmll_
L:
1h
d2vmlb_
B:
1i
d2vmlc_
C:
1j
d2vmld_
D:
1k
d2vmle_
E:
1l
d2vmlf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2vmlB00 (B:1-172)
1b: CATH_2vmlD00 (D:1-172)
1c: CATH_2vmlF00 (F:1-172)
1d: CATH_2vmlH00 (H:1-172)
1e: CATH_2vmlJ00 (J:1-172)
1f: CATH_2vmlL00 (L:1-172)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Globin-like
(786)
Homologous Superfamily
:
Phycocyanins
(32)
Gloeobacter violaceus. Organism_taxid: 33072. Strain: pcc7421.
(4)
1a
2vmlB00
B:1-172
1b
2vmlD00
D:1-172
1c
2vmlF00
F:1-172
1d
2vmlH00
H:1-172
1e
2vmlJ00
J:1-172
1f
2vmlL00
L:1-172
[
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
Chain I
Chain J
Chain K
Chain L
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 (348 KB)
Header - Asym.Unit
Biol.Unit 1 (333 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
2VML
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
