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.
2CZ8
Biol. Unit 2
Info
Asym.Unit (122 KB)
Biol.Unit 1 (170 KB)
Biol.Unit 2 (169 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 TT0972 PROTEIN FROM THERMUS THERMOPHILUS
Authors
:
M. Kumei, E. Inagaki, N. Nakano, A. Shinkai, S. Yokoyama, Riken Struct Genomics/Proteomics Initiative (Rsgi)
Date
:
11 Jul 05 (Deposition) - 19 Sep 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (3x)
Biol. Unit 2: E,F,G,H (3x)
Keywords
:
Dodecamer, Flavin, Flavin-Adenine Dinucleotide, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kumei, E. Inagaki, N. Nakano, A. Shinkai, S. Yokoyama
Crystal Structure Of Tt0972 Protein From Thermus Thermophilus
To Be Published
[
close entry info
]
Hetero Components
(2, 27)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
1c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
1d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
1e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
1f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
1g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
1h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
12
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
PO4
15
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
11: CC2 (SOFTWARE)
12: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
LYS E:6 , VAL E:8 , HOH E:2106 , HOH E:2125 , HOH E:2184 , LYS F:6 , VAL F:8 , LYS G:6 , VAL G:8
BINDING SITE FOR RESIDUE PO4 E 2103
02
AC4
SOFTWARE
LYS H:6
BINDING SITE FOR RESIDUE PO4 H 2104
03
AC7
SOFTWARE
THR F:13 , SER F:14 , GLU F:55 , HOH F:2134 , HOH F:2155 , GLY G:2 , LYS G:3
BINDING SITE FOR RESIDUE PO4 F 2107
04
AC8
SOFTWARE
GLY H:2 , LYS H:3 , THR H:13 , SER H:14 , GLU H:55 , HOH H:2137 , HOH H:2165 , HOH H:2171 , HOH H:2177
BINDING SITE FOR RESIDUE PO4 H 2108
05
AC9
SOFTWARE
GLY E:2 , LYS E:3 , THR G:13 , SER G:14 , GLU G:15 , GLU G:55 , HOH G:2135 , HOH G:2166
BINDING SITE FOR RESIDUE PO4 G 2109
06
BC3
SOFTWARE
GLU E:19
BINDING SITE FOR RESIDUE K E 1152
07
BC4
SOFTWARE
GLU F:19 , GLU G:19 , GLU H:19
BINDING SITE FOR RESIDUE K G 1153
08
BC8
SOFTWARE
ARG B:45 , THR B:47 , ILE B:48 , GLU B:50 , GLN B:57 , FAD C:1203 , LYS D:3 , TYR D:5 , VAL D:11 , ARG D:34 , HIS D:35 , LEU D:36 , ASP D:37 , TRP D:38 , GLN D:57 , ARG D:65 , HOH D:2115 , HOH D:2174 , GLU E:50 , ALA E:51
BINDING SITE FOR RESIDUE FAD D 1204
09
BC9
SOFTWARE
LYS E:3 , TYR E:5 , ARG E:30 , ARG E:34 , HIS E:35 , ASP E:37 , TRP E:38 , ARG E:45 , THR E:47 , GLN E:57 , ARG E:65 , HOH E:2156 , HOH E:2164 , HOH E:2165 , HOH E:2166 , HOH E:2167 , HOH E:2181 , FAD F:1206 , VAL G:11 , GLN G:57 , VAL G:59 , HOH G:2120
BINDING SITE FOR RESIDUE FAD E 1205
10
CC1
SOFTWARE
VAL E:11 , GLN E:57 , FAD E:1205 , LYS F:3 , TYR F:5 , ARG F:30 , LEU F:33 , ARG F:34 , HIS F:35 , LEU F:36 , ASP F:37 , TRP F:38 , ARG F:65 , HOH F:2153 , HOH F:2159 , HOH F:2160 , HOH F:2167 , ARG G:45 , THR G:47 , GLN G:57
BINDING SITE FOR RESIDUE FAD F 1206
11
CC2
SOFTWARE
GLN F:57 , HOH F:2182 , LYS G:3 , TYR G:5 , GLU G:16 , HIS G:35 , ASP G:37 , TRP G:38 , ARG G:65 , HOH G:2122 , HOH G:2147 , HOH G:2164 , HOH G:2165 , HOH G:2176 , HOH G:2180 , ARG H:45 , THR H:47 , GLN H:57 , FAD H:1208
BINDING SITE FOR RESIDUE FAD G 1207
12
CC3
SOFTWARE
ARG F:45 , THR F:47 , GLN F:57 , FAD G:1207 , LYS H:3 , TYR H:5 , VAL H:11 , ARG H:34 , HIS H:35 , LEU H:36 , ASP H:37 , TRP H:38 , GLN H:57 , VAL H:59 , ARG H:65 , HOH H:2118 , HOH H:2181
BINDING SITE FOR RESIDUE FAD H 1208
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2cz8b_ (B:)
1b: SCOP_d2cz8g_ (G:)
1c: SCOP_d2cz8h_ (H:)
1d: SCOP_d2cz8c_ (C:)
1e: SCOP_d2cz8d_ (D:)
1f: SCOP_d2cz8e_ (E:)
1g: SCOP_d2cz8f_ (F:)
2a: SCOP_d2cz8a1 (A:2-68)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Dodecin subunit-like
(56)
Superfamily
:
Dodecin-like
(33)
Family
:
Dodecin-like
(29)
Protein domain
:
automated matches
(24)
Thermus thermophilus HB8 [TaxId: 300852]
(6)
1a
d2cz8b_
B:
1b
d2cz8g_
G:
1c
d2cz8h_
H:
1d
d2cz8c_
C:
1e
d2cz8d_
D:
1f
d2cz8e_
E:
1g
d2cz8f_
F:
Protein domain
:
Uncharacterized protein TTHA1431
(3)
Thermus thermophilus [TaxId: 274]
(3)
2a
d2cz8a1
A:2-68
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2cz8A00 (A:2-68)
1b: CATH_2cz8C00 (C:2-68)
1c: CATH_2cz8G00 (G:2-68)
1d: CATH_2cz8D00 (D:2-69)
1e: CATH_2cz8E00 (E:2-69)
1f: CATH_2cz8H00 (H:2-69)
1g: CATH_2cz8B00 (B:3-68)
1h: CATH_2cz8F00 (F:3-68)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dodecin subunit-like
(24)
Homologous Superfamily
:
Flavin-binding protein dodecin
(24)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(1)
1a
2cz8A00
A:2-68
1b
2cz8C00
C:2-68
1c
2cz8G00
G:2-68
1d
2cz8D00
D:2-69
1e
2cz8E00
E:2-69
1f
2cz8H00
H:2-69
1g
2cz8B00
B:3-68
1h
2cz8F00
F:3-68
[
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 E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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 (122 KB)
Header - Asym.Unit
Biol.Unit 1 (170 KB)
Header - Biol.Unit 1
Biol.Unit 2 (169 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
2CZ8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
