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.
1TU2
Asym. Unit
Info
Asym.Unit (921 KB)
Biol.Unit 1 (95 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(10 )
Title
:
THE COMPLEX OF NOSTOC CYTOCHROME F AND PLASTOCYANIN DETERMIN WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES
Authors
:
I. Diaz-Moreno, A. Diaz-Quintana, M. A. De La Rosa, M. Ubbink
Date
:
24 Jun 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A,B (10 x)
Biol. Unit 1: A,B (1x)
Keywords
:
Electron Transport, Paramagnetic, Chemical Shift, Complex Formation, Dynamic Complex, Photosynthesis, Pseudocontact Shift, Electron Transport Proteins Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Diaz-Moreno, A. Diaz-Quintana, M. A. De La Rosa, M. Ubbink
Structure Of The Complex Between Plastocyanin And Cytochrom F From The Cyanobacterium Nostoc Sp. Pcc 7119 As Determined By Paramagnetic Nmr. The Balance Between Electrostatic And Hydrophobic Interactions Within The Transient Complex Determines The Relative Orientation Of The Two Proteins.
J. Biol. Chem. V. 280 18908 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: COPPER (II) ION (CUa)
2a: HEME C (HECa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CU
1
Ligand/Ion
COPPER (II) ION
2
HEC
1
Ligand/Ion
HEME C
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:39 , CYS A:89 , HIS A:92 , MET A:97
BINDING SITE FOR RESIDUE CU A 106
2
AC2
SOFTWARE
TYR B:1 , PRO B:2 , TRP B:4 , CYS B:22 , CYS B:25 , HIS B:26 , GLN B:60 , LEU B:70 , ASN B:71 , VAL B:72 , GLY B:73 , ALA B:74 , VAL B:75 , ASN B:154 , GLY B:156 , ARG B:157 , GLY B:158 , VAL B:160 , TYR B:161
BINDING SITE FOR RESIDUE HEC B 255
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: COPPER_BLUE (A: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_NOSS1
116-131
1
A: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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1tu2b2 (B:170-235)
2a: SCOP_d1tu2b1 (B:1-169,B:236-254)
3a: SCOP_d1tu2a1 (A:1-105)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Rudiment single hybrid motif
(69)
Family
:
Cytochrome f, small domain
(12)
Protein domain
:
Cytochrome f, small domain
(12)
Nostoc sp. PCC 7120 [TaxId: 103690]
(1)
1a
d1tu2b2
B:170-235
Fold
:
Common fold of diphtheria toxin/transcription factors/cytochrome f
(364)
Superfamily
:
Cytochrome f, large domain
(12)
Family
:
Cytochrome f, large domain
(12)
Protein domain
:
Cytochrome f, large domain
(12)
Nostoc sp. PCC 7120 [TaxId: 103690]
(1)
2a
d1tu2b1
B:1-169,B:236-254
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Plastocyanin/azurin-like
(241)
Protein domain
:
Plastocyanin
(56)
Anabaena variabilis [TaxId: 1172]
(4)
3a
d1tu2a1
A:1-105
[
close SCOP info
]
CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1tu2B02 (B:172-233)
2a: CATH_1tu2B01 (B:1-171,B:234-252)
3a: CATH_1tu2A00 (A:1-105)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
[code=2.40.50.100, no name defined]
(113)
Pcc 7119 (Nostoc sp)
(1)
1a
1tu2B02
B:172-233
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.830, no name defined]
(19)
Pcc 7119 (Nostoc sp)
(1)
2a
1tu2B01
B:1-171,B:234-252
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Pcc 7119 (Nostoc sp)
(1)
3a
1tu2A00
A:1-105
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Copper_bind_1tu2A01 (A:3-104)
2a: PFAM_Apocytochr_F_C_1tu2B01 (B:168-254)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Copper-bind
(82)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(1)
1a
Copper-bind-1tu2A01
A:3-104
Clan
:
Hybrid
(58)
Family
:
Apocytochr_F_C
(5)
Nostoc sp. (strain PCC 7120 / UTEX 2576)
(2)
2a
Apocytochr_F_C-1tu2B01
B:168-254
[
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 (921 KB)
Header - Asym.Unit
Biol.Unit 1 (95 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
1TU2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
