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.
3LDH
Asym. Unit
Info
Asym.Unit (55 KB)
Biol.Unit 1 (178 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
A COMPARISON OF THE STRUCTURES OF APO DOGFISH M4 LACTATE DEHYDROGENASE AND ITS TERNARY COMPLEXES
Authors
:
J. L. White, M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. Lentz I. E. Smiley, S. J. Steindel, M. G. Rossmann
Date
:
06 Jun 74 (Deposition) - 29 Apr 77 (Release) - 01 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (4x)
Keywords
:
Oxidoreductase, Choh Donor, Nad Acceptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. White, M. L. Hackert, M. Buehner, M. J. Adams, G. C. Ford, P. J. Lentz Jr. , I. E. Smiley, S. J. Steindel, M. G. Rossmann
A Comparison Of The Structures Of Apo Dogfish M4 Lactate Dehydrogenase And Its Ternary Complexes.
J. Mol. Biol. V. 102 759 1976
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
3a: PYRUVIC ACID (PYRa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
NAD
1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
3
PYR
1
Ligand/Ion
PYRUVIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:27 , GLY A:28 , CYS A:29 , ASP A:30 , ASP A:53 , VAL A:54 , MET A:55 , GLU A:56 , ASP A:57 , LYS A:58 , LEU A:59 , LYS A:60 , GLU A:62 , SER A:80 , GLY A:81 , LYS A:83 , ASP A:84 , TYR A:85 , THR A:97 , ALA A:98 , GLY A:99 , ARG A:101 , LEU A:137 , HIS A:138 , PRO A:139 , GLU A:140 , SER A:163 , HIS A:195 , TYR A:246 , ALA A:248 , PYR A:333
BINDING SITE FOR RESIDUE NAD A 332
2
AC2
SOFTWARE
LEU A:167 , ARG A:171 , HIS A:195 , NAD A:332
BINDING SITE FOR RESIDUE PYR A 333
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: L_LDH (A:192-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
L_LDH
PS00064
L-lactate dehydrogenase active site.
LDHA_SQUAC
191-197
1
A:192-198
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d3ldha_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Low resolution protein structures
(283)
Fold
:
Proteins of incorrect, partial and unknown sequence
(12)
Superfamily
:
Proteins of incorrect, partial and unknown sequence
(12)
Family
:
Proteins of incorrect, partial and unknown sequence
(12)
Protein domain
:
Lactate dehydrogenase
(1)
Dogfish (Squalus acanthias) [TaxId: 7797]
(1)
1a
d3ldha_
A:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3ldhA01 (A:1-164)
2a: CATH_3ldhA02 (A:165-331)
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)
Spiny dogfish (Squalus acanthias)
(4)
1a
3ldhA01
A:1-164
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)
Spiny dogfish (Squalus acanthias)
(4)
2a
3ldhA02
A:165-331
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ldh_1_C_3ldhA01 (A:165-330)
2a: PFAM_Ldh_1_N_3ldhA02 (A:22-163)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
LDH_C
(56)
Family
:
Ldh_1_C
(51)
Squalus acanthias (Spiny dogfish)
(2)
1a
Ldh_1_C-3ldhA01
A:165-330
Clan
:
NADP_Rossmann
(1239)
Family
:
Ldh_1_N
(51)
Squalus acanthias (Spiny dogfish)
(2)
2a
Ldh_1_N-3ldhA02
A:22-163
[
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
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 (55 KB)
Header - Asym.Unit
Biol.Unit 1 (178 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
3LDH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help