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.
1F3T
Biol. Unit 2
Info
Asym.Unit (253 KB)
Biol.Unit 1 (127 KB)
Biol.Unit 2 (125 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 TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE (ODC) COMPLEXED WITH PUTRESCINE, ODC'S REACTION PRODUCT.
Authors
:
L. K. Jackson, H. B. Brooks, A. L. Osterman, E. J. Goldsmith, M. A. Philli
Date
:
06 Jun 00 (Deposition) - 22 Nov 00 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Beta-Alpha-Barrel, Modified Greek Key Beta-Sheet, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. K. Jackson, H. B. Brooks, A. L. Osterman, E. J. Goldsmith, M. A. Phillips
Altering The Reaction Specificity Of Eukaryotic Ornithine Decarboxylase.
Biochemistry V. 39 11247 2000
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
1d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
2a: 1,4-DIAMINOBUTANE (PUTa)
2b: 1,4-DIAMINOBUTANE (PUTb)
2c: 1,4-DIAMINOBUTANE (PUTc)
2d: 1,4-DIAMINOBUTANE (PUTd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
2
PUT
2
Ligand/Ion
1,4-DIAMINOBUTANE
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC5
SOFTWARE
LYS C:69 , ASP C:88 , ARG C:154 , HIS C:197 , SER C:200 , GLY C:236 , GLY C:237 , GLU C:274 , GLY C:276 , ARG C:277 , TYR C:389 , HOH C:544 , HOH C:582 , PUT C:1006 , CYS D:360
BINDING SITE FOR RESIDUE PLP C 1005
2
AC6
SOFTWARE
LYS C:69 , ARG C:277 , TYR C:331 , ASP C:332 , TYR C:389 , PLP C:1005 , CYS D:360 , HOH D:640
BINDING SITE FOR RESIDUE PUT C 1006
3
AC7
SOFTWARE
CYS C:360 , LYS D:69 , ARG D:154 , HIS D:197 , SER D:200 , GLY D:236 , GLY D:237 , GLU D:274 , GLY D:276 , ARG D:277 , TYR D:389 , HOH D:525 , HOH D:623 , HOH D:879 , PUT D:1008
BINDING SITE FOR RESIDUE PLP D 1007
4
AC8
SOFTWARE
CYS C:360 , TYR D:331 , ASP D:332 , HOH D:692 , PLP D:1007
BINDING SITE FOR RESIDUE PUT D 1008
[
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
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ODR_DC_2_1 (C:66-84,D:66-84)
2: ODR_DC_2_2 (C:222-239,D:222-239)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ODR_DC_2_1
PS00878
Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
DCOR_TRYBB
64-82
2
-
-
C:66-84
D:66-84
2
ODR_DC_2_2
PS00879
Orn/DAP/Arg decarboxylases family 2 signature 2.
DCOR_TRYBB
220-237
2
-
-
C:222-239
D:222-239
[
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, 8)
Info
All SCOP Domains
1a: SCOP_d1f3ta1 (A:14-43,A:284-422)
1b: SCOP_d1f3tb1 (B:14-43,B:284-422)
1c: SCOP_d1f3tc1 (C:14-43,C:284-409)
1d: SCOP_d1f3td1 (D:14-43,D:284-409)
2a: SCOP_d1f3ta2 (A:44-283)
2b: SCOP_d1f3tb2 (B:44-283)
2c: SCOP_d1f3tc2 (C:44-283)
2d: SCOP_d1f3td2 (D:44-283)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
Alanine racemase C-terminal domain-like
(25)
Family
:
Eukaryotic ODC-like
(13)
Protein domain
:
Eukaryotic ornithine decarboxylase (ODC)
(7)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(5)
1a
d1f3ta1
A:14-43,A:284-422
1b
d1f3tb1
B:14-43,B:284-422
1c
d1f3tc1
C:14-43,C:284-409
1d
d1f3td1
D:14-43,D:284-409
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLP-binding barrel
(27)
Family
:
Alanine racemase-like, N-terminal domain
(25)
Protein domain
:
Eukaryotic ornithine decarboxylase
(7)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(5)
2a
d1f3ta2
A:44-283
2b
d1f3tb2
B:44-283
2c
d1f3tc2
C:44-283
2d
d1f3td2
D:44-283
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1f3tA02 (A:46-279)
1b: CATH_1f3tD02 (D:46-279)
1c: CATH_1f3tB02 (B:46-279)
1d: CATH_1f3tC02 (C:46-279)
2a: CATH_1f3tA01 (A:29-45,A:280-409)
2b: CATH_1f3tB01 (B:29-45,B:280-409)
2c: CATH_1f3tD01 (D:29-45,D:280-406)
2d: CATH_1f3tC01 (C:29-45,C:280-406)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Alanine racemase
(53)
Trypanosoma brucei. Organism_taxid: 5691.
(3)
1a
1f3tA02
A:46-279
1b
1f3tD02
D:46-279
1c
1f3tB02
B:46-279
1d
1f3tC02
C:46-279
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Homologous Superfamily
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Trypanosoma brucei. Organism_taxid: 5691.
(3)
2a
1f3tA01
A:29-45,A:280-409
2b
1f3tB01
B:29-45,B:280-409
2c
1f3tD01
D:29-45,D:280-406
2d
1f3tC01
C:29-45,C:280-406
[
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 C
Chain D
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 (253 KB)
Header - Asym.Unit
Biol.Unit 1 (127 KB)
Header - Biol.Unit 1
Biol.Unit 2 (125 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
1F3T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help