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.
5J4T
Biol. Unit 2
Info
Asym.Unit (207 KB)
Biol.Unit 1 (102 KB)
Biol.Unit 2 (101 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF TETRAMERIC JACALIN COMPLEXED WITH GLCNAC BETA-(1,3) GAL-BETA-OME
Authors
:
K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan
Date
:
01 Apr 16 (Deposition) - 08 Feb 17 (Release) - 08 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
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
:
Plant Lectins, Sugar Binding Protein, Galactose Specific Lectin, Beta-Prism I Fold, Post Translational Proteolysis, T-Antigen Binding Protein, Reducing And Non-Reducing Sugars
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. V. Abhinav, K. Sharma, A. Surolia, M. Vijayan
Distortion Of The Ligand Molecule As A Strategy For Modulating Binding Affinity: Further Studies Involving Complexes Of Jacalin With Beta-Substituted Disaccharides.
Iubmb Life V. 69 72 2017
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
2a: METHYL-BETA-GALACTOSE (MBGa)
2b: METHYL-BETA-GALACTOSE (MBGb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
2
MBG
1
Ligand/Ion
METHYL-BETA-GALACTOSE
3
NAG
-1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
8: AD1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
ASN A:110 , GLY A:111 , LEU A:112 , GLN F:3 , SER F:4
binding site for residue EDO A 202
2
AC4
SOFTWARE
TYR C:39 , VAL C:40 , SER E:18 , ASP E:27 , LYS E:45
binding site for residue EDO E 201
3
AC5
SOFTWARE
ALA E:3 , PHE E:4 , ASP E:5 , LYS E:117 , GLY E:118 , TYR E:126
binding site for residue PEG E 202
4
AC6
SOFTWARE
THR E:102 , TRP F:15 , GLY F:16 , HOH F:202 , ASN G:105
binding site for residue EDO F 101
5
AC7
SOFTWARE
TYR C:78 , VAL C:79 , GLY G:1 , TYR G:78 , GLY G:121 , TYR G:122 , TRP G:123 , ASP G:125 , HOH G:309
binding site for residue MBG G 201
6
AC8
SOFTWARE
ALA G:3 , PHE G:4 , LYS G:117 , GLY G:118 , HOH G:301
binding site for residue EDO G 202
7
AC9
SOFTWARE
SER G:46 , PHE G:47
binding site for residue EDO G 203
8
AD1
SOFTWARE
ASN E:105 , THR G:72 , THR G:102 , TRP H:15 , GLY H:16 , HOH H:202 , HOH H:207
binding site for residue EDO H 101
[
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
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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 (207 KB)
Header - Asym.Unit
Biol.Unit 1 (102 KB)
Header - Biol.Unit 1
Biol.Unit 2 (101 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
5J4T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help