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.
1PTJ
Asym. Unit
Info
Asym.Unit (148 KB)
Biol.Unit 1 (142 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 ANALYSIS OF THE DI AND DIII COMPLEX OF TRANSHYDROGENASE WITH A THIO-NICOTINAMIDE NUCLEOTIDE ANALOGUE
Authors
:
A. Singh, J. D. Venning, P. G. Quirk, G. I. Van Boxel, D. J. Rodrigues, S. J. B. Jackson
Date
:
23 Jun 03 (Deposition) - 07 Oct 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.61
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Transhydrogenase, Thio-Nicotinamide, Mitochondria, Proton Translocation, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Singh, J. D. Venning, P. G. Quirk, G. I. Van Boxel, D. J. Rodrigues, S. A. White, J. B. Jackson
Interactions Between Transhydrogenase And Thio-Nicotinamide Analogues Of Nad(H) And Nadp(H) Underline The Importance Of Nucleotide Conformational Changes In Coupling To Proton Translocation
J. Biol. Chem. V. 278 33208 2003
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3a: THIONICOTINAMIDE-ADENINE-DINUCLEOT... (SNDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
NAP
1
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
SND
1
Ligand/Ion
THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:127 , ILE A:128 , SER A:129 , ASP A:135 , SER A:138 , VAL A:180 , GLY A:181 , VAL A:182 , ASP A:202 , VAL A:203 , ARG A:204 , GLY A:234 , GLN A:247 , THR A:264 , ALA A:265 , LEU A:266 , HOH A:532
BINDING SITE FOR RESIDUE SND A 500
2
AC2
SOFTWARE
GLN B:132 , TYR C:55 , GLY C:56 , ALA C:60 , VAL C:87 , ALA C:88 , GLY C:89 , ARG C:90 , MET C:91 , PRO C:92 , GLY C:129 , ALA C:130 , ASN C:131 , ASP C:132 , VAL C:133 , LYS C:164 , ARG C:165 , SER C:166 , GLY C:170 , TYR C:171 , ASP C:190 , ALA C:191 , HOH C:309 , HOH C:317
BINDING SITE FOR RESIDUE NAP C 300
3
AC3
SOFTWARE
ARG B:204 , THR B:264 , ALA B:265 , LEU B:266 , HOH B:447
BINDING SITE FOR RESIDUE GOL B 401
4
AC4
SOFTWARE
LYS A:316 , ARG B:326
BINDING SITE FOR RESIDUE GOL A 402
5
AC5
SOFTWARE
THR A:113 , VAL A:368 , HOH A:518 , HOH A:531
BINDING SITE FOR RESIDUE GOL A 403
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ALADH_PNT_1 (A:4-30,B:4-30,A:4-30,B:4-30)
2: ALADH_PNT_2 (A:177-202,B:177-202,A:177-202,B:17...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALADH_PNT_1
PS00836
Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 1.
PNTAA_RHORT
4-30
2
A:4-30
B:4-30
PNTAA_RHORU
4-30
2
A:4-30
B:4-30
2
ALADH_PNT_2
PS00837
Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2.
PNTAA_RHORT
177-202
2
A:177-202
B:177-202
PNTAA_RHORU
177-202
2
A:177-202
B:177-202
[
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
(3, 5)
Info
All SCOP Domains
1a: SCOP_d1ptjc_ (C:)
2a: SCOP_d1ptja2 (A:1-143,A:327-371)
2b: SCOP_d1ptjb2 (B:1-143,B:327-381)
3a: SCOP_d1ptja1 (A:144-326)
3b: SCOP_d1ptjb1 (B:144-326)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
DHS-like NAD/FAD-binding domain
(176)
Superfamily
:
DHS-like NAD/FAD-binding domain
(176)
Family
:
Transhydrogenase domain III (dIII)
(22)
Protein domain
:
Transhydrogenase domain III (dIII)
(19)
Rhodospirillum rubrum [TaxId: 1085]
(15)
1a
d1ptjc_
C:
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Formate/glycerate dehydrogenase catalytic domain-like
(49)
Family
:
L-alanine dehydrogenase-like
(18)
Protein domain
:
Nicotinamide nucleotide transhydrogenase dI component
(15)
Rhodospirillum rubrum [TaxId: 1085]
(15)
2a
d1ptja2
A:1-143,A:327-371
2b
d1ptjb2
B:1-143,B:327-381
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Formate/glycerate dehydrogenases, NAD-domain
(49)
Protein domain
:
Nicotinamide nucleotide transhydrogenase dI component
(15)
Rhodospirillum rubrum [TaxId: 1085]
(15)
3a
d1ptja1
A:144-326
3b
d1ptjb1
B:144-326
[
close SCOP info
]
CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_1ptjB02 (B:2-143,B:327-372)
1b: CATH_1ptjA02 (A:2-143,A:327-370)
2a: CATH_1ptjA01 (A:144-326)
2b: CATH_1ptjB01 (B:144-326)
3a: CATH_1ptjC00 (C:30-203)
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
:
[code=3.40.50.1770, no name defined]
(22)
Rhodospirillum rubrum. Organism_taxid: 1085.
(1)
1a
1ptjB02
B:2-143,B:327-372
1b
1ptjA02
A:2-143,A:327-370
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Rhodospirillum rubrum. Organism_taxid: 1085.
(1)
2a
1ptjA01
A:144-326
2b
1ptjB01
B:144-326
Homologous Superfamily
:
TPP-binding domain
(120)
Rhodospirillum rubrum. Organism_taxid: 1085.
(1)
3a
1ptjC00
C:30-203
[
close CATH info
]
Pfam Domains
(3, 5)
Info
all PFAM domains
1a: PFAM_PNTB_1ptjC01 (C:30-202)
2a: PFAM_AlaDh_PNT_N_1ptjB01 (B:4-144)
2b: PFAM_AlaDh_PNT_N_1ptjB02 (B:4-144)
3a: PFAM_AlaDh_PNT_C_1ptjB03 (B:153-319)
3b: PFAM_AlaDh_PNT_C_1ptjB04 (B:153-319)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
FAD_DHS
(82)
Family
:
PNTB
(11)
Rhodospirillum rubrum
(9)
1a
PNTB-1ptjC01
C:30-202
Clan
:
Form_Glyc_dh
(56)
Family
:
AlaDh_PNT_N
(24)
Rhodospirillum rubrum
(9)
2a
AlaDh_PNT_N-1ptjB01
B:4-144
2b
AlaDh_PNT_N-1ptjB02
B:4-144
Clan
:
NADP_Rossmann
(1239)
Family
:
AlaDh_PNT_C
(25)
Rhodospirillum rubrum
(9)
3a
AlaDh_PNT_C-1ptjB03
B:153-319
3b
AlaDh_PNT_C-1ptjB04
B:153-319
[
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 B
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 (148 KB)
Header - Asym.Unit
Biol.Unit 1 (142 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
1PTJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help