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.
3PQD
Biol. Unit 2
Info
Asym.Unit (392 KB)
Biol.Unit 1 (196 KB)
Biol.Unit 2 (195 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 L-LACTATE DEHYDROGENASE FROM BACILLUS SUBTILIS COMPLEXED WITH FBP AND NAD+
Authors
:
Y. Zhang, R. M. Garavito
Date
:
26 Nov 10 (Deposition) - 18 Jan 12 (Release) - 18 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.38
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Lactate Dehydrogenase, Fbp, Nad+, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhang, R. M. Garavito
Crystal Structure Of L-Lactate Dehydrogenase From Bacillus Subtilis Complexed With Fbp And Nad+
To Be Published
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPa)
1b: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPb)
1c: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPc)
1d: BETA-FRUCTOSE-1,6-DIPHOSPHATE (FBPd)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FBP
2
Ligand/Ion
BETA-FRUCTOSE-1,6-DIPHOSPHATE
2
NAD
-1
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ARG F:156 , GLN F:168 , ASN F:169 , HIS F:171 , HOH F:347 , ARG H:156 , GLN H:168 , ASN H:169 , HIS H:171
BINDING SITE FOR RESIDUE FBP F 327
2
AC5
SOFTWARE
ARG E:156 , GLN E:168 , ASN E:169 , HIS E:171 , ARG G:156 , GLN G:168 , ASN G:169 , HIS G:171 , HOH G:332 , HOH G:334 , HOH G:335 , HOH G:338 , HOH G:340
BINDING SITE FOR RESIDUE FBP G 327
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: L_LDH (E:175-181,F:175-181,G:175-181,H:17...)
;
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.
LDH_BACSU
175-181
4
-
-
-
-
E:175-181
F:175-181
G:175-181
H:175-181
[
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_d3pqda2 (A:148-312)
1b: SCOP_d3pqdg2 (G:148-314)
1c: SCOP_d3pqdh2 (H:148-314)
1d: SCOP_d3pqdb2 (B:148-315)
1e: SCOP_d3pqdc2 (C:148-312)
1f: SCOP_d3pqdd2 (D:148-314)
1g: SCOP_d3pqde2 (E:148-314)
1h: SCOP_d3pqdf2 (F:148-314)
2a: SCOP_d3pqda1 (A:3-147)
2b: SCOP_d3pqdb1 (B:4-147)
2c: SCOP_d3pqdc1 (C:4-147)
2d: SCOP_d3pqdd1 (D:4-147)
2e: SCOP_d3pqde1 (E:4-147)
2f: SCOP_d3pqdf1 (F:4-147)
2g: SCOP_d3pqdg1 (G:2-147)
2h: SCOP_d3pqdh1 (H:3-147)
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)
Bacillus subtilis [TaxId: 1423]
(3)
1a
d3pqda2
A:148-312
1b
d3pqdg2
G:148-314
1c
d3pqdh2
H:148-314
1d
d3pqdb2
B:148-315
1e
d3pqdc2
C:148-312
1f
d3pqdd2
D:148-314
1g
d3pqde2
E:148-314
1h
d3pqdf2
F:148-314
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)
Bacillus subtilis [TaxId: 1423]
(11)
2a
d3pqda1
A:3-147
2b
d3pqdb1
B:4-147
2c
d3pqdc1
C:4-147
2d
d3pqdd1
D:4-147
2e
d3pqde1
E:4-147
2f
d3pqdf1
F:4-147
2g
d3pqdg1
G:2-147
2h
d3pqdh1
H:3-147
[
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 E
Chain F
Chain G
Chain H
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 (392 KB)
Header - Asym.Unit
Biol.Unit 1 (196 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 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
3PQD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
