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.
2VYX
Asym. Unit
Info
Asym.Unit (173 KB)
Biol.Unit 1 (162 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 THE T. THERMOPHILUS DODECIN W38F MUTANT
Authors
:
L. -O. Essen, B. Meissner
Date
:
29 Jul 08 (Deposition) - 17 Nov 09 (Release) - 25 Aug 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
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
:
Dodecins, Coenzyme A, Flavin Dimer, Flavoprotein, Hypothetical Protein, Flavin Binding Protein, Protein Binding Putative Storage Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. G. Gurzadyan, B. Meissner, B. Sander, L. -O. Essen, M. E. Michel-Beyerle
Ultrafast Charge Transfer Dynamics In Flavoprotein Dodecin
To Be Published
[
close entry info
]
Hetero Components
(4, 29)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: COENZYME A (COAa)
2b: COENZYME A (COAb)
2c: COENZYME A (COAc)
2d: COENZYME A (COAd)
2e: COENZYME A (COAe)
2f: COENZYME A (COAf)
2g: COENZYME A (COAg)
2h: COENZYME A (COAh)
2i: COENZYME A (COAi)
2j: COENZYME A (COAj)
2k: COENZYME A (COAk)
2l: COENZYME A (COAl)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
3b: FLAVIN MONONUCLEOTIDE (FMNb)
3c: FLAVIN MONONUCLEOTIDE (FMNc)
3d: FLAVIN MONONUCLEOTIDE (FMNd)
3e: FLAVIN MONONUCLEOTIDE (FMNe)
3f: FLAVIN MONONUCLEOTIDE (FMNf)
3g: FLAVIN MONONUCLEOTIDE (FMNg)
3h: FLAVIN MONONUCLEOTIDE (FMNh)
3i: FLAVIN MONONUCLEOTIDE (FMNi)
3j: FLAVIN MONONUCLEOTIDE (FMNj)
3k: FLAVIN MONONUCLEOTIDE (FMNk)
3l: FLAVIN MONONUCLEOTIDE (FMNl)
4a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
COA
12
Ligand/Ion
COENZYME A
3
FMN
12
Ligand/Ion
FLAVIN MONONUCLEOTIDE
4
NA
1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:5 , ASP A:37 , PHE A:38 , ARG A:65 , FMN A:1072 , HOH A:2023 , HOH A:2036 , ARG B:45 , THR B:47 , GLN B:57
BINDING SITE FOR RESIDUE FMN A1070
02
AC2
SOFTWARE
ARG A:28 , THR A:32 , ARG A:34 , HIS A:35 , PHE A:64 , ARG A:65 , LEU A:66 , GLU A:67 , COA A:1073 , HOH A:2037 , HOH A:2038 , HOH A:2039 , LYS H:6 , LYS L:6 , VAL L:8 , ARG L:28 , LEU L:33 , PHE L:64 , LEU L:66 , COA L:1068
BINDING SITE FOR RESIDUE COA A1071
03
AC3
SOFTWARE
FMN A:1070 , HOH A:2040 , HOH A:2041 , HOH A:2042 , GLN B:57 , LYS G:3 , TYR G:5 , ASP G:37 , PHE G:38 , ARG G:65 , ARG H:45 , THR H:47 , GLN H:57
BINDING SITE FOR RESIDUE FMN A1072
04
AC4
SOFTWARE
LYS A:6 , VAL A:8 , LEU A:33 , PHE A:64 , LEU A:66 , COA A:1071 , GLU F:16 , ARG H:28 , THR H:32 , LEU H:33 , ARG H:34 , HIS H:35 , PHE H:64 , ARG H:65 , GLU H:67 , LYS L:6 , LEU L:66 , COA L:1068
BINDING SITE FOR RESIDUE COA A1073
05
AC5
SOFTWARE
LYS A:6 , HOH A:2002 , LYS H:6 , LYS L:6
BINDING SITE FOR RESIDUE CL A1074
06
AC6
SOFTWARE
LYS B:3 , TYR B:5 , ASP B:37 , PHE B:38 , ARG B:65 , FMN B:1070 , HOH B:2045 , ARG C:45 , THR C:47 , GLN C:57 , VAL F:11 , GLN F:57
BINDING SITE FOR RESIDUE FMN B1068
07
AC7
SOFTWARE
ARG B:28 , THR B:32 , LEU B:33 , ARG B:34 , HIS B:35 , PHE B:64 , ARG B:65 , GLU B:67 , HOH B:2047 , HOH B:2048 , HOH B:2050 , LYS F:6 , LEU F:66 , COA F:1071 , LYS G:6 , VAL G:8 , LEU G:66 , COA G:1070
BINDING SITE FOR RESIDUE COA B1069
08
AC8
SOFTWARE
FMN B:1068 , HOH B:2051 , VAL C:11 , LYS E:3 , TYR E:5 , ASP E:37 , PHE E:38 , ARG E:65 , ARG F:45 , THR F:47 , GLN F:57
BINDING SITE FOR RESIDUE FMN B1070
09
AC9
SOFTWARE
LYS B:6 , LYS F:6 , LYS G:6
BINDING SITE FOR RESIDUE CL B1071
10
BC1
SOFTWARE
ARG A:45 , THR A:47 , GLN A:57 , TYR C:5 , ASP C:37 , PHE C:38 , ARG C:65 , FMN C:1072 , HOH C:2021 , HOH C:2044 , GLN J:57
BINDING SITE FOR RESIDUE FMN C1070
11
BC2
SOFTWARE
ARG C:28 , THR C:32 , ARG C:34 , HIS C:35 , PHE C:64 , ARG C:65 , LEU C:66 , GLU C:67 , HOH C:2045 , HOH C:2046 , HOH C:2047 , HOH C:2048 , HOH C:2049 , LYS E:6 , VAL E:8 , ARG E:28 , LEU E:33 , LEU E:66 , COA E:1070 , LYS J:6 , LEU J:66 , COA J:1070
BINDING SITE FOR RESIDUE COA C1071
12
BC3
SOFTWARE
GLN A:57 , FMN C:1070 , HOH C:2050 , HOH C:2051 , HOH C:2052 , ARG J:45 , THR J:47 , GLN J:57 , LYS L:3 , TYR L:5 , ASP L:37 , PHE L:38 , ARG L:65 , HOH L:2010
BINDING SITE FOR RESIDUE FMN C1072
13
BC4
SOFTWARE
LYS C:6 , LYS E:6 , LYS J:6
BINDING SITE FOR RESIDUE CL C1073
14
BC5
SOFTWARE
LYS D:3 , TYR D:5 , ASP D:37 , PHE D:38 , ARG D:65 , FMN D:1072 , HOH D:2026 , HOH D:2048 , HOH D:2049 , HOH D:2050 , HOH D:2051 , ARG E:45 , THR E:47 , GLN E:57 , GLN K:57
BINDING SITE FOR RESIDUE FMN D1070
15
BC6
SOFTWARE
ARG D:28 , THR D:32 , ARG D:34 , ARG D:65 , LEU D:66 , GLU D:67 , HOH D:2021 , HOH D:2054 , LYS I:6 , VAL I:8 , PHE I:64 , LEU I:66 , COA I:1070 , LYS K:6 , COA K:1070 , HOH K:2018 , HOH K:2032
BINDING SITE FOR RESIDUE COA D1071
16
BC7
SOFTWARE
FMN D:1070 , HOH D:2055 , HOH D:2056 , ARG E:45 , GLN E:57 , TYR J:5 , ASP J:37 , PHE J:38 , ARG J:65 , HOH J:2021 , ARG K:45 , THR K:47 , GLN K:57
BINDING SITE FOR RESIDUE FMN D1072
17
BC8
SOFTWARE
LYS D:6 , LYS I:6 , LYS K:6
BINDING SITE FOR RESIDUE CL D1073
18
BC9
SOFTWARE
HIS B:35 , ARG B:65 , HOH B:2040 , LYS C:6 , COA C:1071 , ARG E:28 , THR E:32 , LEU E:33 , ARG E:34 , HIS E:35 , PHE E:64 , ARG E:65 , GLU E:67 , HOH E:2015 , HOH E:2042 , HOH E:2043 , LYS J:6 , VAL J:8 , LEU J:33 , PHE J:64 , LEU J:66 , COA J:1070
BINDING SITE FOR RESIDUE COA E1070
19
CC1
SOFTWARE
ARG D:45 , THR D:47 , GLN D:57 , LYS F:3 , TYR F:5 , ASP F:37 , PHE F:38 , ARG F:65 , FMN F:1072 , HOH F:2021 , HOH F:2024 , HOH F:2042 , HOH F:2044 , GLN G:57
BINDING SITE FOR RESIDUE FMN F1070
20
CC2
SOFTWARE
LYS B:6 , VAL B:8 , ALA B:29 , LEU B:66 , COA B:1069 , HOH B:2047 , ARG F:28 , THR F:32 , LEU F:33 , ARG F:34 , HIS F:35 , ARG F:65 , LEU F:66 , GLU F:67 , HOH F:2013 , HOH F:2023 , HOH F:2046 , LYS G:6 , LEU G:66 , COA G:1070
BINDING SITE FOR RESIDUE COA F1071
21
CC3
SOFTWARE
GLN D:57 , FMN F:1070 , HOH F:2047 , HOH F:2048 , HOH F:2049 , HOH F:2050 , HOH F:2052 , ARG G:45 , THR G:47 , GLN G:57 , TYR I:5 , ASP I:37 , PHE I:38 , ARG I:65 , HOH I:2022
BINDING SITE FOR RESIDUE FMN F1072
22
CC4
SOFTWARE
HOH D:2031 , HOH D:2039 , HOH F:2044
BINDING SITE FOR RESIDUE NA F1073
23
CC5
SOFTWARE
LYS B:6 , LEU B:66 , COA B:1069 , HOH B:2030 , ARG D:65 , LYS F:6 , VAL F:8 , LEU F:33 , PHE F:64 , LEU F:66 , COA F:1071 , ARG G:28 , THR G:32 , LEU G:33 , ARG G:34 , HIS G:35 , PHE G:64 , ARG G:65 , LEU G:66 , GLU G:67 , HOH G:2048 , HOH G:2049 , HOH G:2050
BINDING SITE FOR RESIDUE COA G1070
24
CC6
SOFTWARE
HIS C:35 , TYR H:5 , ASP H:37 , PHE H:38 , ARG H:65 , FMN H:1071 , HOH H:2032 , HOH H:2033 , HOH H:2034 , HOH H:2035 , ARG I:45 , THR I:47 , GLN I:57 , HOH I:2028 , GLN L:57
BINDING SITE FOR RESIDUE FMN H1070
25
CC7
SOFTWARE
FMN H:1070 , HOH H:2036 , HOH H:2037 , GLN I:57 , LYS K:3 , TYR K:5 , ASP K:37 , PHE K:38 , ARG K:65 , HOH K:2017 , ARG L:45 , THR L:47 , GLN L:57
BINDING SITE FOR RESIDUE FMN H1071
26
CC8
SOFTWARE
LYS D:6 , COA D:1071 , HOH D:2006 , ARG I:28 , THR I:32 , LEU I:33 , ARG I:34 , HIS I:35 , PHE I:64 , ARG I:65 , GLU I:67 , HOH I:2043 , LYS K:6 , VAL K:8 , LEU K:10 , LEU K:33 , PHE K:64 , LEU K:66 , COA K:1070
BINDING SITE FOR RESIDUE COA I1070
27
CC9
SOFTWARE
LYS C:6 , VAL C:8 , ALA C:29 , LEU C:33 , PHE C:64 , LEU C:66 , COA C:1071 , LYS E:6 , LEU E:66 , COA E:1070 , ARG J:28 , THR J:32 , LEU J:33 , ARG J:34 , HIS J:35 , ARG J:65 , GLU J:67 , HOH J:2042
BINDING SITE FOR RESIDUE COA J1070
28
DC1
SOFTWARE
LYS D:6 , VAL D:8 , ARG D:28 , PHE D:64 , LEU D:66 , COA D:1071 , LYS I:6 , COA I:1070 , ARG K:28 , THR K:32 , ARG K:34 , HIS K:35 , PHE K:64 , ARG K:65 , GLU K:67 , HOH K:2033 , HOH K:2034
BINDING SITE FOR RESIDUE COA K1070
29
DC2
SOFTWARE
LYS A:6 , LEU A:66 , COA A:1071 , COA A:1073 , HOH A:2038 , ALA D:51 , LYS H:6 , VAL H:8 , PHE H:64 , LEU H:66 , ARG L:28 , THR L:32 , ARG L:34 , HIS L:35 , PHE L:64 , ARG L:65 , GLU L:67 , HOH L:2027
BINDING SITE FOR RESIDUE COA L1068
[
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_d2vyxa_ (A:)
1b: SCOP_d2vyxb_ (B:)
1c: SCOP_d2vyxc_ (C:)
1d: SCOP_d2vyxd_ (D:)
1e: SCOP_d2vyxe_ (E:)
1f: SCOP_d2vyxf_ (F:)
1g: SCOP_d2vyxg_ (G:)
1h: SCOP_d2vyxh_ (H:)
1i: SCOP_d2vyxi_ (I:)
1j: SCOP_d2vyxj_ (J:)
1k: SCOP_d2vyxk_ (K:)
1l: SCOP_d2vyxl_ (L:)
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
d2vyxa_
A:
1b
d2vyxb_
B:
1c
d2vyxc_
C:
1d
d2vyxd_
D:
1e
d2vyxe_
E:
1f
d2vyxf_
F:
1g
d2vyxg_
G:
1h
d2vyxh_
H:
1i
d2vyxi_
I:
1j
d2vyxj_
J:
1k
d2vyxk_
K:
1l
d2vyxl_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2vyxA00 (A:2-69)
1b: CATH_2vyxC00 (C:2-69)
1c: CATH_2vyxD00 (D:2-69)
1d: CATH_2vyxE00 (E:2-69)
1e: CATH_2vyxF00 (F:2-69)
1f: CATH_2vyxG00 (G:2-69)
1g: CATH_2vyxH00 (H:2-69)
1h: CATH_2vyxI00 (I:2-69)
1i: CATH_2vyxJ00 (J:2-69)
1j: CATH_2vyxK00 (K:2-69)
1k: CATH_2vyxB00 (B:2-67)
1l: CATH_2vyxL00 (L:2-67)
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. Organism_taxid: 300852. Strain: hb8.
(5)
1a
2vyxA00
A:2-69
1b
2vyxC00
C:2-69
1c
2vyxD00
D:2-69
1d
2vyxE00
E:2-69
1e
2vyxF00
F:2-69
1f
2vyxG00
G:2-69
1g
2vyxH00
H:2-69
1h
2vyxI00
I:2-69
1i
2vyxJ00
J:2-69
1j
2vyxK00
K:2-69
1k
2vyxB00
B:2-67
1l
2vyxL00
L:2-67
[
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 (173 KB)
Header - Asym.Unit
Biol.Unit 1 (162 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
2VYX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
