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.
3FOO
Biol. Unit 4
Info
Asym.Unit (227 KB)
Biol.Unit 1 (57 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (57 KB)
Biol.Unit 4 (57 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A TRIANGULAR CYTOCHROME B562 SUPERSTRUCTURE MEDIATED BY NI COORDINATION - MONOCLINIC FORM
Authors
:
R. J. Radford, F. A. Tezcan
Date
:
30 Dec 08 (Deposition) - 14 Jul 09 (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 (1x)
Biol. Unit 2: D,E,F (1x)
Biol. Unit 3: G,H,I (1x)
Biol. Unit 4: J,K,L (1x)
Keywords
:
Four Helix Bundle, Electron Transport, Heme, Iron, Metal-Binding, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. J. Radford, F. A. Tezcan
A Superprotein Triangle Driven By Nickel(Ii) Coordination: Exploiting Non-Natural Metal Ligands In Protein Self-Assembly
J. Am. Chem. Soc. V. 131 9136 2009
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
1g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
1h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
1i: PROTOPORPHYRIN IX CONTAINING FE (HEMi)
1j: PROTOPORPHYRIN IX CONTAINING FE (HEMj)
1k: PROTOPORPHYRIN IX CONTAINING FE (HEMk)
1l: PROTOPORPHYRIN IX CONTAINING FE (HEMl)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
2c: NICKEL (II) ION (NIc)
2d: NICKEL (II) ION (NId)
2e: NICKEL (II) ION (NIe)
2f: NICKEL (II) ION (NIf)
2g: NICKEL (II) ION (NIg)
2h: NICKEL (II) ION (NIh)
2i: NICKEL (II) ION (NIi)
2j: NICKEL (II) ION (NIj)
2k: NICKEL (II) ION (NIk)
2l: NICKEL (II) ION (NIl)
2m: NICKEL (II) ION (NIm)
2n: NICKEL (II) ION (NIn)
2o: NICKEL (II) ION (NIo)
2p: NICKEL (II) ION (NIp)
2q: NICKEL (II) ION (NIq)
2r: NICKEL (II) ION (NIr)
2s: NICKEL (II) ION (NIs)
2t: NICKEL (II) ION (NIt)
2u: NICKEL (II) ION (NIu)
2v: NICKEL (II) ION (NIv)
2w: NICKEL (II) ION (NIw)
2x: NICKEL (II) ION (NIx)
3a: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXa)
3b: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXb)
3c: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXc)
3d: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXd)
3e: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXe)
3f: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXf)
3g: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXg)
3h: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXh)
3i: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXi)
3j: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXj)
3k: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXk)
3l: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
3
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NI
-1
Ligand/Ion
NICKEL (II) ION
3
PXX
3
Ligand/Ion
N-1,10-PHENANTHROLIN-5-YLACETAMIDE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: EC1 (SOFTWARE)
02: EC2 (SOFTWARE)
03: EC3 (SOFTWARE)
04: EC4 (SOFTWARE)
05: EC5 (SOFTWARE)
06: EC6 (SOFTWARE)
07: EC7 (SOFTWARE)
08: EC8 (SOFTWARE)
09: EC9 (SOFTWARE)
10: FC1 (SOFTWARE)
11: FC2 (SOFTWARE)
12: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
EC1
SOFTWARE
GLU J:4 , MET J:7 , ASN J:11 , PRO J:45 , PRO J:46 , PHE J:61 , PHE J:65 , CYS J:98 , CYS J:101 , HIS J:102 , TYR J:105 , ARG J:106
BINDING SITE FOR RESIDUE HEM J 150
02
EC2
SOFTWARE
GLN J:41 , LYS J:42 , ALA J:43 , PRO J:53 , MET J:58 , CYS J:59 , ALA J:62 , ASP L:73 , ASP L:74 , HIS L:77 , NI L:108
BINDING SITE FOR RESIDUE PXX J 151
03
EC3
SOFTWARE
ALA J:1 , ASP J:39 , HOH J:182
BINDING SITE FOR RESIDUE NI J 107
04
EC4
SOFTWARE
HIS J:77 , HOH K:112 , HOH K:113 , PXX K:151
BINDING SITE FOR RESIDUE NI J 108
05
EC5
SOFTWARE
GLU K:4 , MET K:7 , ASN K:11 , MET K:33 , PRO K:46 , PHE K:61 , PHE K:65 , CYS K:98 , CYS K:101 , HIS K:102 , TYR K:105 , ARG K:106
BINDING SITE FOR RESIDUE HEM K 150
06
EC6
SOFTWARE
ASP J:74 , HIS J:77 , NI J:108 , GLN K:41 , LYS K:42 , ALA K:43 , PRO K:53 , MET K:58 , CYS K:59 , HOH K:112
BINDING SITE FOR RESIDUE PXX K 151
07
EC7
SOFTWARE
ALA K:1 , ASP K:39
BINDING SITE FOR RESIDUE NI K 107
08
EC8
SOFTWARE
HIS K:77 , HOH K:128 , HOH K:129 , PXX L:151
BINDING SITE FOR RESIDUE NI K 108
09
EC9
SOFTWARE
GLU L:4 , MET L:7 , PRO L:45 , PRO L:46 , PHE L:61 , PHE L:65 , THR L:97 , CYS L:98 , CYS L:101 , HIS L:102 , ARG L:106
BINDING SITE FOR RESIDUE HEM L 150
10
FC1
SOFTWARE
ASP K:73 , ASP K:74 , HIS K:77 , NI K:108 , GLN L:41 , LYS L:42 , ALA L:43 , PRO L:53 , MET L:58 , CYS L:59
BINDING SITE FOR RESIDUE PXX L 151
11
FC2
SOFTWARE
ALA L:1 , ASP L:39 , HOH L:194
BINDING SITE FOR RESIDUE NI L 107
12
FC3
SOFTWARE
HOH J:126 , PXX J:151 , HIS L:77 , HOH L:127
BINDING SITE FOR RESIDUE NI L 108
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3fooa_ (A:)
1b: SCOP_d3foob_ (B:)
1c: SCOP_d3fooc_ (C:)
1d: SCOP_d3food_ (D:)
1e: SCOP_d3fooe_ (E:)
1f: SCOP_d3foof_ (F:)
1g: SCOP_d3foog_ (G:)
1h: SCOP_d3fooh_ (H:)
1i: SCOP_d3fooi_ (I:)
1j: SCOP_d3fooj_ (J:)
1k: SCOP_d3fook_ (K:)
1l: SCOP_d3fool_ (L:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Cytochromes
(82)
Family
:
Cytochrome b562
(38)
Protein domain
:
automated matches
(32)
Escherichia coli [TaxId: 562]
(31)
1a
d3fooa_
A:
1b
d3foob_
B:
1c
d3fooc_
C:
1d
d3food_
D:
1e
d3fooe_
E:
1f
d3foof_
F:
1g
d3foog_
G:
1h
d3fooh_
H:
1i
d3fooi_
I:
1j
d3fooj_
J:
1k
d3fook_
K:
1l
d3fool_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3fooA00 (A:1-106)
1b: CATH_3fooB00 (B:1-106)
1c: CATH_3fooC00 (C:1-106)
1d: CATH_3fooD00 (D:1-106)
1e: CATH_3fooE00 (E:1-106)
1f: CATH_3fooF00 (F:1-106)
1g: CATH_3fooG00 (G:1-106)
1h: CATH_3fooH00 (H:1-106)
1i: CATH_3fooI00 (I:1-106)
1j: CATH_3fooJ00 (J:1-106)
1k: CATH_3fooK00 (K:1-106)
1l: CATH_3fooL00 (L:1-106)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.10, no name defined]
(45)
Escherichia coli. Organism_taxid: 562.
(13)
1a
3fooA00
A:1-106
1b
3fooB00
B:1-106
1c
3fooC00
C:1-106
1d
3fooD00
D:1-106
1e
3fooE00
E:1-106
1f
3fooF00
F:1-106
1g
3fooG00
G:1-106
1h
3fooH00
H:1-106
1i
3fooI00
I:1-106
1j
3fooJ00
J:1-106
1k
3fooK00
K:1-106
1l
3fooL00
L:1-106
[
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 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 (227 KB)
Header - Asym.Unit
Biol.Unit 1 (57 KB)
Header - Biol.Unit 1
Biol.Unit 2 (57 KB)
Header - Biol.Unit 2
Biol.Unit 3 (57 KB)
Header - Biol.Unit 3
Biol.Unit 4 (57 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
3FOO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help