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.
1SMK
Biol. Unit 3
Info
Asym.Unit (384 KB)
Biol.Unit 1 (100 KB)
Biol.Unit 2 (100 KB)
Biol.Unit 3 (99 KB)
Biol.Unit 4 (98 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MATURE AND TRANSLOCATABLE FORMS OF GLYOXYSOMAL MALATE DEHYDROGENASE HAVE DIFFERENT ACTIVITIES AND STABILITIES BUT SIMILAR CRYSTAL STRUCTURES
Authors
:
B. Cox, M. M. Chit, T. Weaver, J. Bailey, C. Gietl, E. Bell, L. Banaszak
Date
:
09 Mar 04 (Deposition) - 25 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Tricarboxylic Cycle, Glyoxysome, Nad, Glyoxylate Bypass, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Cox, M. M. Chit, T. Weaver, C. Gietl, J. Bailey, E. Bell, L. Banaszak
Organelle And Translocatable Forms Of Glyoxysomal Malate Dehydrogenase. The Effect Of The N-Terminal Presequence.
Febs J. V. 272 643 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MDH (E:189-201,F:189-201)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MDH
PS00068
Malate dehydrogenase active site signature.
MDHG_CITLA
189-201
2
-
-
-
-
E:189-201
F:189-201
-
-
[
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, 16)
Info
All SCOP Domains
1a: SCOP_d1smka2 (A:189-356)
1b: SCOP_d1smkb2 (B:189-356)
1c: SCOP_d1smkc2 (C:189-356)
1d: SCOP_d1smkd2 (D:189-356)
1e: SCOP_d1smke2 (E:189-356)
1f: SCOP_d1smkf2 (F:189-356)
1g: SCOP_d1smkg2 (G:189-356)
1h: SCOP_d1smkh2 (H:189-356)
2a: SCOP_d1smka1 (A:44-188)
2b: SCOP_d1smkb1 (B:44-188)
2c: SCOP_d1smkc1 (C:44-188)
2d: SCOP_d1smkd1 (D:44-188)
2e: SCOP_d1smke1 (E:44-188)
2f: SCOP_d1smkf1 (F:44-188)
2g: SCOP_d1smkg1 (G:44-188)
2h: SCOP_d1smkh1 (H:44-188)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
LDH C-terminal domain-like
(172)
Superfamily
:
LDH C-terminal domain-like
(172)
Family
:
automated matches
(38)
Protein domain
:
automated matches
(38)
Citrullus lanatus [TaxId: 3654]
(2)
1a
d1smka2
A:189-356
1b
d1smkb2
B:189-356
1c
d1smkc2
C:189-356
1d
d1smkd2
D:189-356
1e
d1smke2
E:189-356
1f
d1smkf2
F:189-356
1g
d1smkg2
G:189-356
1h
d1smkh2
H:189-356
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
automated matches
(447)
Protein domain
:
automated matches
(447)
Citrullus lanatus [TaxId: 3654]
(2)
2a
d1smka1
A:44-188
2b
d1smkb1
B:44-188
2c
d1smkc1
C:44-188
2d
d1smkd1
D:44-188
2e
d1smke1
E:44-188
2f
d1smkf1
F:44-188
2g
d1smkg1
G:44-188
2h
d1smkh1
H:44-188
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1smkA01 (A:44-189)
1b: CATH_1smkB01 (B:44-189)
1c: CATH_1smkC01 (C:44-189)
1d: CATH_1smkD01 (D:44-189)
1e: CATH_1smkE01 (E:44-189)
1f: CATH_1smkF01 (F:44-189)
1g: CATH_1smkG01 (G:44-189)
1h: CATH_1smkH01 (H:44-189)
2a: CATH_1smkA02 (A:190-356)
2b: CATH_1smkB02 (B:190-356)
2c: CATH_1smkC02 (C:190-356)
2d: CATH_1smkD02 (D:190-356)
2e: CATH_1smkE02 (E:190-356)
2f: CATH_1smkF02 (F:190-356)
2g: CATH_1smkG02 (G:190-356)
2h: CATH_1smkH02 (H:190-356)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Citrullus lanatus. Organism_taxid: 3654.
(2)
1a
1smkA01
A:44-189
1b
1smkB01
B:44-189
1c
1smkC01
C:44-189
1d
1smkD01
D:44-189
1e
1smkE01
E:44-189
1f
1smkF01
F:44-189
1g
1smkG01
G:44-189
1h
1smkH01
H:44-189
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2
(116)
Homologous Superfamily
:
L-2-Hydroxyisocaproate Dehydrogenase, subunit A, domain 2
(116)
Citrullus lanatus. Organism_taxid: 3654.
(2)
2a
1smkA02
A:190-356
2b
1smkB02
B:190-356
2c
1smkC02
C:190-356
2d
1smkD02
D:190-356
2e
1smkE02
E:190-356
2f
1smkF02
F:190-356
2g
1smkG02
G:190-356
2h
1smkH02
H:190-356
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1smkH01 (H:190-354)
1b: PFAM_Ldh_1_C_1smkH02 (H:190-354)
1c: PFAM_Ldh_1_C_1smkH03 (H:190-354)
1d: PFAM_Ldh_1_C_1smkH04 (H:190-354)
1e: PFAM_Ldh_1_C_1smkH05 (H:190-354)
1f: PFAM_Ldh_1_C_1smkH06 (H:190-354)
1g: PFAM_Ldh_1_C_1smkH07 (H:190-354)
1h: PFAM_Ldh_1_C_1smkH08 (H:190-354)
2a: PFAM_Ldh_1_N_1smkH09 (H:45-188)
2b: PFAM_Ldh_1_N_1smkH10 (H:45-188)
2c: PFAM_Ldh_1_N_1smkH11 (H:45-188)
2d: PFAM_Ldh_1_N_1smkH12 (H:45-188)
2e: PFAM_Ldh_1_N_1smkH13 (H:45-188)
2f: PFAM_Ldh_1_N_1smkH14 (H:45-188)
2g: PFAM_Ldh_1_N_1smkH15 (H:45-188)
2h: PFAM_Ldh_1_N_1smkH16 (H:45-188)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Citrullus lanatus (Watermelon) (Citrullus vulgaris)
(2)
1a
Ldh_1_C-1smkH01
H:190-354
1b
Ldh_1_C-1smkH02
H:190-354
1c
Ldh_1_C-1smkH03
H:190-354
1d
Ldh_1_C-1smkH04
H:190-354
1e
Ldh_1_C-1smkH05
H:190-354
1f
Ldh_1_C-1smkH06
H:190-354
1g
Ldh_1_C-1smkH07
H:190-354
1h
Ldh_1_C-1smkH08
H:190-354
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Citrullus lanatus (Watermelon) (Citrullus vulgaris)
(2)
2a
Ldh_1_N-1smkH09
H:45-188
2b
Ldh_1_N-1smkH10
H:45-188
2c
Ldh_1_N-1smkH11
H:45-188
2d
Ldh_1_N-1smkH12
H:45-188
2e
Ldh_1_N-1smkH13
H:45-188
2f
Ldh_1_N-1smkH14
H:45-188
2g
Ldh_1_N-1smkH15
H:45-188
2h
Ldh_1_N-1smkH16
H:45-188
[
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
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 (384 KB)
Header - Asym.Unit
Biol.Unit 1 (100 KB)
Header - Biol.Unit 1
Biol.Unit 2 (100 KB)
Header - Biol.Unit 2
Biol.Unit 3 (99 KB)
Header - Biol.Unit 3
Biol.Unit 4 (98 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
1SMK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help