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.
1VKE
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (110 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 CARBOXYMUCONOLACTONE DECARBOXYLASE FAMILY PROTEIN POSSIBLY INVOLVED IN ANTIOXIDATIVE RESPONSE (TM1620) FROM THERMOTOGA MARITIMA AT 1.56 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
13 May 04 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.56
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Tm1620, Carboxymuconolactone Decarboxylase Family Protein Possibly Involved In Antioxidative Response, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Carboxymuconolactone Decarboxylase Family Protein Possibly Involved In Antioxidative Response (Tm1620) From Thermotoga Maritima At 1. 56 A Resolution
To Be Published
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2a: UNKNOWN LIGAND (UNLa)
2b: UNKNOWN LIGAND (UNLb)
2c: UNKNOWN LIGAND (UNLc)
2d: UNKNOWN LIGAND (UNLd)
2e: UNKNOWN LIGAND (UNLe)
2f: UNKNOWN LIGAND (UNLf)
2g: UNKNOWN LIGAND (UNLg)
2h: UNKNOWN LIGAND (UNLh)
2i: UNKNOWN LIGAND (UNLi)
2j: UNKNOWN LIGAND (UNLj)
2k: UNKNOWN LIGAND (UNLk)
2l: UNKNOWN LIGAND (UNLl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MPD
1
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
2
UNL
12
Ligand/Ion
UNKNOWN LIGAND
[
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
ARG A:58 , CYS A:59 , ASP A:60 , ASP A:61 , HIS A:98 , HOH A:143 , HOH A:154 , HOH A:197 , HIS E:98 , ARG E:101
BINDING SITE FOR RESIDUE UNL A 122
02
AC2
SOFTWARE
HOH A:197 , HIS B:98 , ARG B:101 , ARG E:58 , CYS E:59 , ASP E:60 , ASP E:61 , HIS E:98 , HOH E:145 , HOH E:148 , HOH E:194
BINDING SITE FOR RESIDUE UNL E 122
03
AC3
SOFTWARE
HIS A:98 , ARG A:101 , ARG B:58 , CYS B:59 , ASP B:60 , ASP B:61 , HIS B:98 , HOH B:135 , HOH B:171
BINDING SITE FOR RESIDUE UNL B 122
04
AC4
SOFTWARE
ARG C:58 , CYS C:59 , ASP C:60 , ASP C:61 , HIS C:98 , HOH C:156 , HOH C:179 , HOH D:185 , HIS F:98 , ARG F:101
BINDING SITE FOR RESIDUE UNL C 122
05
AC5
SOFTWARE
HIS C:98 , ARG C:101 , ARG D:58 , CYS D:59 , ASP D:60 , ASP D:61 , HIS D:98 , HOH D:145 , HOH D:146 , HOH D:185
BINDING SITE FOR RESIDUE UNL D 122
06
AC6
SOFTWARE
HIS D:98 , ARG D:101 , ARG F:58 , CYS F:59 , ASP F:60 , ASP F:61 , HIS F:98 , HOH F:130 , HOH F:173
BINDING SITE FOR RESIDUE UNL F 122
07
AC7
SOFTWARE
LEU C:57 , ARG C:58 , HOH C:185 , LEU D:57 , ARG D:58
BINDING SITE FOR RESIDUE UNL C 123
08
AC8
SOFTWARE
SER B:93 , ASP E:32 , TYR E:36 , SER E:54 , CYS E:62 , HIS E:66 , VAL F:90
BINDING SITE FOR RESIDUE UNL E 123
09
AC9
SOFTWARE
SER A:93 , ASP B:32 , TYR B:36 , HIS B:66 , HOH B:198 , VAL C:90
BINDING SITE FOR RESIDUE UNL B 123
10
BC1
SOFTWARE
ASP A:32 , TYR A:36 , CYS A:62 , HIS A:66 , SER E:93
BINDING SITE FOR RESIDUE UNL A 123
11
BC2
SOFTWARE
TYR C:36 , SER C:54 , HIS C:66
BINDING SITE FOR RESIDUE UNL C 124
12
BC3
SOFTWARE
SER D:93 , ASP F:32 , TYR F:36 , SER F:54 , HIS F:66
BINDING SITE FOR RESIDUE UNL F 123
13
BC4
SOFTWARE
VAL A:90 , SER C:93 , ASP D:32 , TYR D:36 , SER D:54 , CYS D:62 , HIS D:66
BINDING SITE FOR RESIDUE MPD D 123
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d1vkea_ (A:)
1b: SCOP_d1vkeb_ (B:)
1c: SCOP_d1vkec_ (C:)
1d: SCOP_d1vked_ (D:)
1e: SCOP_d1vkee_ (E:)
1f: SCOP_d1vkef_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
AhpD-like
(17)
Superfamily
:
AhpD-like
(17)
Family
:
CMD-like
(3)
Protein domain
:
Hypothetical protein TM1620
(2)
Thermotoga maritima [TaxId: 2336]
(2)
1a
d1vkea_
A:
1b
d1vkeb_
B:
1c
d1vkec_
C:
1d
d1vked_
D:
1e
d1vkee_
E:
1f
d1vkef_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1vkeE00 (E:2-121)
1b: CATH_1vkeA00 (A:4-121)
1c: CATH_1vkeB00 (B:21-121)
1d: CATH_1vkeD00 (D:19-119)
1e: CATH_1vkeC00 (C:21-120)
1f: CATH_1vkeF00 (F:20-116)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
AhpD-like
(17)
Homologous Superfamily
:
AhpD-like
(17)
Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8.
(1)
1a
1vkeE00
E:2-121
1b
1vkeA00
A:4-121
1c
1vkeB00
B:21-121
1d
1vkeD00
D:19-119
1e
1vkeC00
C:21-120
1f
1vkeF00
F:20-116
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_CMD_1vkeF01 (F:23-108)
1b: PFAM_CMD_1vkeF02 (F:23-108)
1c: PFAM_CMD_1vkeF03 (F:23-108)
1d: PFAM_CMD_1vkeF04 (F:23-108)
1e: PFAM_CMD_1vkeF05 (F:23-108)
1f: PFAM_CMD_1vkeF06 (F:23-108)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
AhpD-like
(9)
Family
:
CMD
(9)
Thermotoga maritima
(2)
1a
CMD-1vkeF01
F:23-108
1b
CMD-1vkeF02
F:23-108
1c
CMD-1vkeF03
F:23-108
1d
CMD-1vkeF04
F:23-108
1e
CMD-1vkeF05
F:23-108
1f
CMD-1vkeF06
F:23-108
[
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
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 (119 KB)
Header - Asym.Unit
Biol.Unit 1 (110 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
1VKE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
