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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4BMB
Asym. Unit
Info
Asym.Unit (61 KB)
Biol.Unit 1 (57 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 THE N TERMINAL DOMAIN OF HUMAN GALECTIN 8
Authors
:
E. Buzamet, F. M. Ruiz, M. Menendez, A. Romero, H. J. Gabius, D. Solis
Date
:
07 May 13 (Deposition) - 19 Mar 14 (Release) - 19 Mar 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Sugar Binding Protein, Carbohydrate Recognition
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. M. Ruiz, B. A. Scholz, E. Buzamet, J. Kopitz, S. Andre, M. Menendez, A. Romero, D. Solis, H. J. Gabius
Natural Single Amino Acid Polymorphism (F19Y) In Human Galectin-8: Detection Of Structural Alterations And Increased Growth-Regulatory Activity On Tumor Cells.
Febs J. V. 281 1446 2014
[
close entry info
]
Hetero Components
(4, 4)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: BETA-LACTOSE (LATa)
3a: SODIUM ION (NAa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
LAT
1
Ligand/Ion
BETA-LACTOSE
3
NA
1
Ligand/Ion
SODIUM ION
4
ZN
1
Ligand/Ion
ZINC 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
ASP A:25 , HIS A:38 , HIS A:147 , HOH A:2099 , HOH A:2100
BINDING SITE FOR RESIDUE ZN A1154
2
AC2
SOFTWARE
ARG A:45 , HIS A:65 , ASN A:67 , ARG A:69 , ASN A:79 , TRP A:86 , GLU A:89 , NA A:1156 , HOH A:2150 , HOH A:2182 , HOH A:2183 , HOH A:2242 , HOH A:2243 , HOH A:2244 , HOH A:2245 , HOH A:2246
BINDING SITE FOR RESIDUE LAT A1155
3
AC3
SOFTWARE
GLN A:47 , ARG A:59 , LAT A:1155 , HOH A:2248
BINDING SITE FOR RESIDUE NA A1156
4
AC4
SOFTWARE
ARG A:59 , TYR A:141 , HOH A:2121 , HOH A:2122 , HOH A:2249
BINDING SITE FOR RESIDUE GOL A1157
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_012990 (F19Y, chain A, )
2: VAR_009710 (R36C, chain A, )
3: VAR_012991 (M56V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_012990
F
19
Y
LEG8_HUMAN
Polymorphism
2737713
A
F
19
Y
2
UniProt
VAR_009710
R
36
C
LEG8_HUMAN
Polymorphism
1041935
A
R
36
C
3
UniProt
VAR_012991
M
56
V
LEG8_HUMAN
Polymorphism
1041937
A
M
56
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: GALECTIN (A:19-152|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GALECTIN
PS51304
Galactoside-binding lectin (galectin) domain profile.
LEG8_HUMAN
19-152
187-317
1
A:19-152
-
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.6a (A:4-15)
Exon 1.7b (A:16-45)
Exon 1.8b (A:45-115)
Exon 1.9b (A:116-153)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3c/1.6a
2: Boundary 1.6a/1.7b
3: Boundary 1.7b/1.8b
4: Boundary 1.8b/1.9b
5: Boundary 1.9b/1.10e
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
1.3c
ENST00000366584
3c
ENSE00001381502
chr1:
236686899-236687361
463
LEG8_HUMAN
-
0
0
-
-
1.6a
ENST00000366584
6a
ENSE00002193374
chr1:
236689268-236689415
148
LEG8_HUMAN
1-15
15
1
A:4-15
12
1.7b
ENST00000366584
7b
ENSE00002141991
chr1:
236700797-236700885
89
LEG8_HUMAN
16-45
30
1
A:16-45
30
1.8b
ENST00000366584
8b
ENSE00000793501
chr1:
236702179-236702389
211
LEG8_HUMAN
45-115
71
1
A:45-115
71
1.9b
ENST00000366584
9b
ENSE00000805377
chr1:
236703864-236703983
120
LEG8_HUMAN
116-155
40
1
A:116-153
38
1.10e
ENST00000366584
10e
ENSE00000793503
chr1:
236704954-236705010
57
LEG8_HUMAN
156-174
19
0
-
-
1.11c
ENST00000366584
11c
ENSE00001226656
chr1:
236706061-236706087
27
LEG8_HUMAN
175-183
9
0
-
-
1.11r
ENST00000366584
11r
ENSE00002191373
chr1:
236706860-236706948
89
LEG8_HUMAN
184-213
30
0
-
-
1.12c
ENST00000366584
12c
ENSE00000805385
chr1:
236708050-236708215
166
LEG8_HUMAN
213-268
56
0
-
-
1.14j
ENST00000366584
14j
ENSE00001911385
chr1:
236711312-236714310
2999
LEG8_HUMAN
269-317
49
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4bmba_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
automated matches
(133)
Protein domain
:
automated matches
(133)
Human (Homo sapiens) [TaxId: 9606]
(36)
1a
d4bmba_
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 (61 KB)
Header - Asym.Unit
Biol.Unit 1 (57 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
4BMB
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help