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.
1OD5
Asym. Unit
Info
Asym.Unit (133 KB)
Biol.Unit 1 (375 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 GLYCININ A3B4 SUBUNIT HOMOHEXAMER
Authors
:
M. Adachi, J. Kanamori, T. Masuda, K. Yagasaki, K. Kitamura, B. Mikami, S. Utsumi
Date
:
13 Feb 03 (Deposition) - 02 Jun 03 (Release) - 10 Jun 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Glycinin, Soybean, Globulin, 11S, Seed Storage Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Adachi, J. Kanamori, T. Masuda, K. Yagasaki, K. Kitamura, B. Mikami, S. Utsumi
Crystal Structure Of Soybean 11S Globulin: Glycinin A3B4 Homohexamer
Proc. Natl. Acad. Sci. Usa V. 100 7395 2003
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: CARBONATE ION (CO3a)
1b: CARBONATE ION (CO3b)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO3
2
Ligand/Ion
CARBONATE ION
2
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:50 , HIS A:58 , TYR A:131 , THR A:133 , HOH A:2102
BINDING SITE FOR RESIDUE CO3 A 496
2
AC2
SOFTWARE
HIS B:383 , GLU B:432 , TYR B:441 , HOH B:2083
BINDING SITE FOR RESIDUE MG A 498
3
AC3
SOFTWARE
ARG B:50 , HIS B:58 , TYR B:131 , THR B:133 , HOH B:2112
BINDING SITE FOR RESIDUE CO3 B 497
4
AC4
SOFTWARE
HIS A:383 , GLU A:432 , TYR A:441
BINDING SITE FOR RESIDUE MG B 499
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: 11S_SEED_STORAGE (A:321-342,B:321-342)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
11S_SEED_STORAGE
PS00305
11-S plant seed storage proteins signature.
GLYG5_SOYBN
344-366
2
A:321-342
B:321-342
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1od5a1 (A:7-251)
1b: SCOP_d1od5a2 (A:321-493)
1c: SCOP_d1od5b1 (B:7-251)
1d: SCOP_d1od5b2 (B:321-493)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
RmlC-like cupins
(220)
Family
:
Germin/Seed storage 7S protein
(34)
Protein domain
:
Seed storage 7S protein
(18)
Soybean (Glycine max), glycinin A3B4 [TaxId: 3847]
(1)
1a
d1od5a1
A:7-251
1b
d1od5a2
A:321-493
1c
d1od5b1
B:7-251
1d
d1od5b2
B:321-493
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1od5A02 (A:336-493)
1b: CATH_1od5B02 (B:336-493)
1c: CATH_1od5A01 (A:7-335)
1d: CATH_1od5B01 (B:7-335)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
Jelly Rolls
(177)
Soybean (Glycine max)
(10)
1a
1od5A02
A:336-493
1b
1od5B02
B:336-493
1c
1od5A01
A:7-335
1d
1od5B01
B:7-335
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cupin_1_1od5B01 (B:333-479)
1b: PFAM_Cupin_1_1od5B02 (B:333-479)
1c: PFAM_Cupin_1_1od5B03 (B:333-479)
1d: PFAM_Cupin_1_1od5B04 (B:333-479)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cupin
(179)
Family
:
Cupin_1
(15)
Glycine max (Soybean) (Glycine hispida)
(5)
1a
Cupin_1-1od5B01
B:333-479
1b
Cupin_1-1od5B02
B:333-479
1c
Cupin_1-1od5B03
B:333-479
1d
Cupin_1-1od5B04
B:333-479
[
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
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 (133 KB)
Header - Asym.Unit
Biol.Unit 1 (375 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
1OD5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
