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.
1UR5
Asym. Unit
Info
Asym.Unit (110 KB)
Biol.Unit 1 (206 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STABILIZATION OF A TETRAMERIC MALATE DEHYDROGENASE BY INTRODUCTION OF A DISULFIDE BRIDGE AT THE DIMER/DIMER INTERFACE
Authors
:
A. Bjork, B. Dalhus, D. Mantzilas, V. G. H. Eijsink, R. Sirevag
Date
:
27 Oct 03 (Deposition) - 05 Nov 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,C
Biol. Unit 1: A,C (2x)
Keywords
:
Oxidoreductase, Tricarboxylic Acid Cycle, Malate Dehydrogenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Bjork, B. Dalhus, D. Mantzilas, V. G. H. Eijsink, R. Sirevag
Stabilization Of A Tetrameric Malate Dehydrogenase By Introduction Of A Disulfide Bridge At The Dimer-Dimer Interface
J. Mol. Biol. V. 334 811 2003
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: CADMIUM ION (CDa)
1b: CADMIUM ION (CDb)
1c: CADMIUM ION (CDc)
1d: CADMIUM ION (CDd)
1e: CADMIUM ION (CDe)
1f: CADMIUM ION (CDf)
2a: CHLORIDE ION (CLa)
4a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
4b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CD
6
Ligand/Ion
CADMIUM ION
2
CL
1
Ligand/Ion
CHLORIDE ION
3
NA
2
Ligand/Ion
SODIUM ION
4
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:178 , CL A:1312 , HOH A:2156 , HOH A:2157
BINDING SITE FOR RESIDUE CD A1309
02
AC2
SOFTWARE
GLU A:165 , HOH C:2203 , HOH C:2211
BINDING SITE FOR RESIDUE CD A1310
03
AC3
SOFTWARE
ASP A:200 , ASP A:243 , GLU A:277 , HOH A:2238
BINDING SITE FOR RESIDUE CD A1311
04
AC4
SOFTWARE
ASP A:123 , ALA A:124 , CD A:1309
BINDING SITE FOR RESIDUE CL A1312
05
AC5
SOFTWARE
HIS A:19
BINDING SITE FOR RESIDUE NA A1313
06
AC6
SOFTWARE
GLU C:178 , HOH C:2083 , HOH C:2113 , HOH C:2115
BINDING SITE FOR RESIDUE CD C1310
07
AC7
SOFTWARE
HOH A:2212 , GLU C:165
BINDING SITE FOR RESIDUE CD C1311
08
AC8
SOFTWARE
GLU A:159 , HOH A:2139 , GLU C:159 , HOH C:2140
BINDING SITE FOR RESIDUE CD C1312
09
AC9
SOFTWARE
HIS C:19
BINDING SITE FOR RESIDUE NA C1313
10
BC1
SOFTWARE
GLY A:9 , GLY A:11 , PHE A:12 , VAL A:13 , ASP A:33 , ILE A:34 , VAL A:35 , TYR A:65 , THR A:77 , SER A:78 , GLY A:79 , VAL A:118 , ASN A:119 , ASN A:120 , LEU A:147 , HIS A:175 , ALA A:225 , PRO A:229 , HOH A:2277 , HOH A:2278 , HOH A:2279 , HOH A:2280 , HOH A:2281 , HOH A:2282
BINDING SITE FOR RESIDUE NAD A1308
11
BC2
SOFTWARE
GLY C:9 , GLY C:11 , PHE C:12 , VAL C:13 , ASP C:33 , ILE C:34 , VAL C:35 , TYR C:65 , THR C:77 , SER C:78 , GLY C:79 , ALA C:80 , CYS C:102 , VAL C:118 , ASN C:120 , LEU C:147 , HIS C:175 , PRO C:229 , HOH C:2197 , HOH C:2262 , HOH C:2263 , HOH C:2264 , HOH C:2265
BINDING SITE FOR RESIDUE NAD C1309
[
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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ur5a2 (A:144-308)
1b: SCOP_d1ur5c2 (C:144-309)
2a: SCOP_d1ur5a1 (A:2-143)
2b: SCOP_d1ur5c1 (C:2-143)
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
:
Lactate & malate dehydrogenases, C-terminal domain
(125)
Protein domain
:
Malate dehydrogenase
(37)
Chloroflexus aurantiacus [TaxId: 1108]
(7)
1a
d1ur5a2
A:144-308
1b
d1ur5c2
C:144-309
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
:
LDH N-terminal domain-like
(117)
Protein domain
:
Malate dehydrogenase
(39)
Chloroflexus aurantiacus [TaxId: 1108]
(7)
2a
d1ur5a1
A:2-143
2b
d1ur5c1
C:2-143
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ur5C01 (C:2-144)
1b: CATH_1ur5A01 (A:2-144)
2a: CATH_1ur5A02 (A:145-305)
2b: CATH_1ur5C02 (C:145-305)
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)
Chloroflexus aurantiacus. Organism_taxid: 1108.
(7)
1a
1ur5C01
C:2-144
1b
1ur5A01
A:2-144
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)
Chloroflexus aurantiacus. Organism_taxid: 1108.
(7)
2a
1ur5A02
A:145-305
2b
1ur5C02
C:145-305
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_1ur5C01 (C:145-309)
1b: PFAM_Ldh_1_C_1ur5C02 (C:145-309)
2a: PFAM_Ldh_1_N_1ur5C03 (C:3-143)
2b: PFAM_Ldh_1_N_1ur5C04 (C:3-143)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
(6)
1a
Ldh_1_C-1ur5C01
C:145-309
1b
Ldh_1_C-1ur5C02
C:145-309
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
(6)
2a
Ldh_1_N-1ur5C03
C:3-143
2b
Ldh_1_N-1ur5C04
C:3-143
[
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 C
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 (110 KB)
Header - Asym.Unit
Biol.Unit 1 (206 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
1UR5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help