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.
4CL3
Biol. Unit 1
Info
Asym.Unit (224 KB)
Biol.Unit 1 (425 KB)
Biol.Unit 2 (215 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
1.70 A RESOLUTION STRUCTURE OF THE MALATE DEHYDROGENASE FROM CHLOROFLEXUS AURANTIACUS
Authors
:
R. Talon, D. Madern, E. Girard
Date
:
11 Jan 14 (Deposition) - 05 Feb 14 (Release) - 19 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,D
Biol. Unit 1: A,D (2x)
Biol. Unit 2: A,D (1x)
Keywords
:
Thermophile, Oxidoreductase, Tricarboxylic Acid Cycle
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Talon, N. Coquelle, D. Madern, E. Girard
An Experimental Point Of View On Hydration/Solvation In Halophilic Proteins.
Front. Microbiol. V. 5 66 2014
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 18)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
2a: CADMIUM ION (CDa)
2b: CADMIUM ION (CDb)
2c: CADMIUM ION (CDc)
2d: CADMIUM ION (CDd)
2e: CADMIUM ION (CDe)
2f: CADMIUM ION (CDf)
2g: CADMIUM ION (CDg)
2h: CADMIUM ION (CDh)
2i: CADMIUM ION (CDi)
2j: CADMIUM ION (CDj)
2k: CADMIUM ION (CDk)
3a: CHLORIDE ION (CLa)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
10
Ligand/Ion
ACETATE ION
2
CD
-1
Ligand/Ion
CADMIUM ION
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
PEG
8
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:165 , HOH A:2284 , HOH A:2285 , HOH A:2288 , HOH A:2289 , HOH A:2466
BINDING SITE FOR RESIDUE CD A1310
02
AC2
SOFTWARE
ASP A:33 , ACT A:1317 , HOH A:2057 , HOH A:2467
BINDING SITE FOR RESIDUE CD A1311
03
AC3
SOFTWARE
ASP A:90 , HOH A:2166 , HOH A:2170 , HOH A:2468
BINDING SITE FOR RESIDUE CD A1312
04
AC4
SOFTWARE
GLU A:159 , ARG A:201 , HOH A:2272 , HOH A:2274 , GLU D:159 , HOH D:2289
BINDING SITE FOR RESIDUE CD A1313
05
AC5
SOFTWARE
GLU A:281 , HOH A:2469
BINDING SITE FOR RESIDUE CD A1314
06
AC6
SOFTWARE
ARG A:208 , HOH A:2034
BINDING SITE FOR RESIDUE CL A1315
07
AC7
SOFTWARE
PRO A:121 , ASP A:123 , ALA A:124 , GLU A:178 , THR A:302 , HOH A:2232
BINDING SITE FOR RESIDUE ACT A1316
08
AC8
SOFTWARE
ILE A:8 , GLY A:9 , ASP A:33 , ILE A:34 , TYR A:65 , SER A:78 , CD A:1311
BINDING SITE FOR RESIDUE ACT A1317
09
AC9
SOFTWARE
PHE D:12 , LEU D:220 , THR D:222 , GLY D:223 , SER D:224 , TYR D:226 , PEG D:1319 , HOH D:2472 , HOH D:2473 , HOH D:2474 , HOH D:2475
BINDING SITE FOR RESIDUE PEG A1318
10
BC1
SOFTWARE
ARG A:100 , GLU A:131 , VAL A:132
BINDING SITE FOR RESIDUE PEG A1319
11
BC2
SOFTWARE
GLY A:214 , VAL A:217 , ASN A:218 , HOH A:2360 , HOH A:2362
BINDING SITE FOR RESIDUE PEG A1320
12
BC3
SOFTWARE
HOH A:2382 , HOH A:2383 , GLU D:165 , HOH D:2096 , HOH D:2297 , HOH D:2447
BINDING SITE FOR RESIDUE CD D1310
13
BC4
SOFTWARE
ASP D:33 , ACT D:1318 , PEG D:1319
BINDING SITE FOR RESIDUE CD D1311
14
BC5
SOFTWARE
GLU D:89 , ASP D:90 , HOH D:2183
BINDING SITE FOR RESIDUE CD D1312
15
BC6
SOFTWARE
ASP D:200 , ASP D:243 , GLU D:277 , HOH D:2338
BINDING SITE FOR RESIDUE CD D1313
16
BC7
SOFTWARE
GLU D:36
BINDING SITE FOR RESIDUE CD D1314
17
BC8
SOFTWARE
ASP D:177
BINDING SITE FOR RESIDUE CD D1315
18
BC9
SOFTWARE
HOH A:2272 , HOH A:2279 , GLU D:159 , ILE D:197 , ALA D:198 , ARG D:201 , HOH D:2339
BINDING SITE FOR RESIDUE ACT D1316
19
CC1
SOFTWARE
LYS D:24 , GLU D:53 , ALA D:234 , GLN D:235 , HOH D:2033 , HOH D:2092
BINDING SITE FOR RESIDUE ACT D1317
20
CC2
SOFTWARE
ILE D:8 , GLY D:9 , ASP D:33 , ILE D:34 , SER D:78 , CD D:1311 , HOH D:2449
BINDING SITE FOR RESIDUE ACT D1318
21
CC3
SOFTWARE
PEG A:1318 , ALA D:10 , GLY D:11 , ASP D:33 , VAL D:38 , LYS D:42 , CD D:1311 , HOH D:2075 , HOH D:2448 , HOH D:2450
BINDING SITE FOR RESIDUE PEG D1319
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d4cl3a2 (A:144-309)
1b: SCOP_d4cl3d2 (D:144-309)
2a: SCOP_d4cl3a1 (A:1-143)
2b: SCOP_d4cl3d1 (D:1-143)
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 sp. [TaxId: 480224]
(1)
1a
d4cl3a2
A:144-309
1b
d4cl3d2
D: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 sp. [TaxId: 480224]
(1)
2a
d4cl3a1
A:1-143
2b
d4cl3d1
D:1-143
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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 D
Asymmetric Unit 1
Asymmetric Unit 2
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 (224 KB)
Header - Asym.Unit
Biol.Unit 1 (425 KB)
Header - Biol.Unit 1
Biol.Unit 2 (215 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
4CL3
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help