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.
2Q5B
Asym. Unit
Info
Asym.Unit (114 KB)
Biol.Unit 1 (38 KB)
Biol.Unit 2 (38 KB)
Biol.Unit 3 (38 KB)
Biol.Unit 4 (109 KB)
Biol.Unit 5 (110 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH RESOLUTION STRUCTURE OF PLASTOCYANIN FROM PHORMIDIUM LAMINOSUM
Authors
:
R. Fromme, Y. S. Bukhman-Deruyter, I. Grotjohann, H. Mi, P. Fromme
Date
:
31 May 07 (Deposition) - 17 Jun 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: A,B,C (1x)
Biol. Unit 5: A,B,C (1x)
Keywords
:
Plastocyanin, Electron Transport, Photosystem 1
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. S. Bukhman-Deruyter, R. Fromme, I. Grotjohann, B. Schlarb-Ridley H. Mi, P. Fromme
Plastocyanin At High Resolution From Phormidium Laminosum And The Double Mutant D44A, D45A
To Be Published
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: COPPER (II) ION (CUa)
2b: COPPER (II) ION (CUb)
2c: COPPER (II) ION (CUc)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
3e: POTASSIUM ION (Ke)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
CU
3
Ligand/Ion
COPPER (II) ION
3
K
5
Ligand/Ion
POTASSIUM ION
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:38 , HIS A:39 , CYS A:89 , HIS A:92 , MET A:97
BINDING SITE FOR RESIDUE CU A 106
02
AC2
SOFTWARE
ASP A:44 , ASP A:45 , HOH A:613 , HIS B:61 , HOH B:507
BINDING SITE FOR RESIDUE ZN A 107
03
AC3
SOFTWARE
HIS B:39 , CYS B:89 , HIS B:92 , MET B:97
BINDING SITE FOR RESIDUE CU B 106
04
AC4
SOFTWARE
ASP B:45 , HIS C:61 , HOH C:595
BINDING SITE FOR RESIDUE ZN B 107
05
AC5
SOFTWARE
HIS C:39 , CYS C:89 , HIS C:92 , MET C:97
BINDING SITE FOR RESIDUE CU C 106
06
AC6
SOFTWARE
HIS A:61 , ASP C:44 , ASP C:45 , HOH C:505 , HOH C:511
BINDING SITE FOR RESIDUE ZN C 107
07
AC7
SOFTWARE
HIS A:24 , GLU A:104 , HIS C:24 , GLU C:104 , HOH C:582
BINDING SITE FOR RESIDUE ZN C 108
08
AC8
SOFTWARE
GLN B:15 , PHE B:16 , GLY B:96
BINDING SITE FOR RESIDUE K B 502
09
AC9
SOFTWARE
LEU C:42 , ASP C:44 , GLN C:47 , THR C:86 , TYR C:88 , HOH C:513
BINDING SITE FOR RESIDUE K C 501
10
BC1
SOFTWARE
TYR A:88 , HOH A:607 , GLN B:63 , LEU B:64
BINDING SITE FOR RESIDUE K A 502
11
BC2
SOFTWARE
LEU A:42 , PHE A:43 , ASP A:44 , GLN A:47 , THR A:86 , TYR A:88
BINDING SITE FOR RESIDUE K A 501
12
BC3
SOFTWARE
GLN C:15 , PHE C:16
BINDING SITE FOR RESIDUE K C 502
13
BC4
SOFTWARE
LEU A:64 , GLU A:70 , ASP C:44 , ARG C:93
BINDING SITE FOR RESIDUE ACT A 601
[
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, 3)
Info
All PROSITE Patterns/Profiles
1: COPPER_BLUE (A:82-97,B:82-97,C:82-97)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
COPPER_BLUE
PS00196
Type-1 copper (blue) proteins signature.
PLAS_PHOLA
116-131
3
A:82-97
B:82-97
C:82-97
[
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, 3)
Info
All SCOP Domains
1a: SCOP_d2q5ba_ (A:)
1b: SCOP_d2q5bb_ (B:)
1c: SCOP_d2q5bc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Plastocyanin/azurin-like
(241)
Protein domain
:
Plastocyanin
(56)
Phormidium laminosum [TaxId: 32059]
(8)
1a
d2q5ba_
A:
1b
d2q5bb_
B:
1c
d2q5bc_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2q5bA00 (A:1-105)
1b: CATH_2q5bB00 (B:1-105)
1c: CATH_2q5bC00 (C:1-105)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Phormidium laminosum.
(1)
1a
2q5bA00
A:1-105
1b
2q5bB00
B:1-105
1c
2q5bC00
C:1-105
[
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
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 (114 KB)
Header - Asym.Unit
Biol.Unit 1 (38 KB)
Header - Biol.Unit 1
Biol.Unit 2 (38 KB)
Header - Biol.Unit 2
Biol.Unit 3 (38 KB)
Header - Biol.Unit 3
Biol.Unit 4 (109 KB)
Header - Biol.Unit 4
Biol.Unit 5 (110 KB)
Header - Biol.Unit 5
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
2Q5B
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help