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.
3AGI
Asym. Unit
Info
Asym.Unit (59 KB)
Biol.Unit 1 (54 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HIGH RESOLUTION X-RAY ANALYSIS OF ARG-LYSOZYME COMPLEX IN THE PRESENCE OF 500 MM ARG
Authors
:
L. Ito, K. Shiraki, K. Hasegawa, S. Baba, T. Kumasaka
Date
:
31 Mar 10 (Deposition) - 23 Mar 11 (Release) - 23 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase, Lysozyme, Glycosidase, Arginine, Allergen, Antimicrobial, Bacteriolytic Enzyme, Disulfide Bond
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Ito, K. Shiraki, T. Matsuura, M. Okumura, K. Hasegawa, S. Baba, H. Yamaguchi, T. Kumasaka
High-Resolution X-Ray Analysis Reveals Binding Of Arginine To Aromatic Residues Of Lysozyme Surface: Implication Of Suppression Of Protein Aggregation By Arginine
Protein Eng. Des. Sel. V. 24 269 2011
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: ARGININE (ARGa)
2b: ARGININE (ARGb)
2c: ARGININE (ARGc)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
4a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
ARG
3
Mod. Amino Acid
ARGININE
3
CL
8
Ligand/Ion
CHLORIDE ION
4
NA
1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:57 , ILE A:58 , ASN A:59 , TRP A:63 , ALA A:107 , TRP A:108 , HOH A:242
BINDING SITE FOR RESIDUE ACT A 130
02
AC2
SOFTWARE
TRP A:62 , ASP A:101 , ARG A:125 , HOH A:154 , HOH A:157 , HOH A:242 , HOH A:244 , HOH A:317
BINDING SITE FOR RESIDUE ARG A 131
03
AC3
SOFTWARE
ARG A:5 , GLY A:117 , ALA A:122 , TRP A:123 , HOH A:161 , HOH A:174 , HOH A:228 , HOH A:263 , HOH A:281
BINDING SITE FOR RESIDUE ARG A 132
04
AC4
SOFTWARE
ARG A:21 , GLY A:22 , GLU A:35 , ASP A:52 , TRP A:108 , VAL A:109 , ALA A:110 , CL A:142 , HOH A:172 , HOH A:220 , HOH A:221 , HOH A:240 , HOH A:304
BINDING SITE FOR RESIDUE ARG A 133
05
AC5
SOFTWARE
SER A:60 , CYS A:64 , SER A:72 , ARG A:73 , HOH A:197 , HOH A:215
BINDING SITE FOR RESIDUE NA A 134
06
AC6
SOFTWARE
ASN A:65 , GLY A:67 , ARG A:68 , THR A:69
BINDING SITE FOR RESIDUE CL A 135
07
AC7
SOFTWARE
SER A:24 , GLY A:26 , GLN A:121 , HOH A:250
BINDING SITE FOR RESIDUE CL A 136
08
AC8
SOFTWARE
ASN A:19 , SER A:24 , LEU A:25 , HOH A:144 , HOH A:268
BINDING SITE FOR RESIDUE CL A 137
09
AC9
SOFTWARE
SER A:85 , ASP A:87 , THR A:89 , ALA A:90 , HOH A:209 , HOH A:254
BINDING SITE FOR RESIDUE CL A 138
10
BC1
SOFTWARE
GLY A:22 , TYR A:23 , SER A:24 , ASN A:27 , ARG A:114 , HOH A:152
BINDING SITE FOR RESIDUE CL A 139
11
BC2
SOFTWARE
ARG A:14 , ILE A:88
BINDING SITE FOR RESIDUE CL A 140
12
BC3
SOFTWARE
TRP A:111 , ARG A:114 , HOH A:177 , HOH A:218
BINDING SITE FOR RESIDUE CL A 141
13
BC4
SOFTWARE
TYR A:23 , ASN A:113 , ARG A:133
BINDING SITE FOR RESIDUE CL A 142
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: LACTALBUMIN_LYSOZYME_2 (A:1-129)
2: LACTALBUMIN_LYSOZYME_1 (A:76-94)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LACTALBUMIN_LYSOZYME_2
PS51348
Alpha-lactalbumin / lysozyme C family profile.
LYSC_CHICK
19-147
1
A:1-129
2
LACTALBUMIN_LYSOZYME_1
PS00128
Alpha-lactalbumin / lysozyme C signature.
LYSC_CHICK
94-112
1
A:76-94
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.1a (A:1-28)
Exon 1.2 (A:28-82)
Exon 1.3 (A:82-108)
Exon 1.4a (A:108-129)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4a
5: Boundary 1.4a/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENSGALT00000016196
1a
ENSGALE00000107726
chr1:
37298007-37298210
204
LYSC_CHICK
1-46
46
1
A:1-28
28
1.2
ENSGALT00000016196
2
ENSGALE00000107723
chr1:
37299463-37299624
162
LYSC_CHICK
46-100
55
1
A:28-82
55
1.3
ENSGALT00000016196
3
ENSGALE00000107724
chr1:
37301396-37301474
79
LYSC_CHICK
100-126
27
1
A:82-108
27
1.4a
ENSGALT00000016196
4a
ENSGALE00000107725
chr1:
37301556-37301734
179
LYSC_CHICK
126-147
22
1
A:108-129
22
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3agia_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Lysozyme-like
(1361)
Superfamily
:
Lysozyme-like
(1361)
Family
:
C-type lysozyme
(738)
Protein domain
:
Lysozyme
(696)
Chicken (Gallus gallus) [TaxId: 9031]
(459)
1a
d3agia_
A:
[
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 A
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 (59 KB)
Header - Asym.Unit
Biol.Unit 1 (54 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
3AGI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
