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.
2ZHM
Asym. Unit
Info
Asym.Unit (113 KB)
Biol.Unit 1 (30 KB)
Biol.Unit 2 (30 KB)
Biol.Unit 3 (29 KB)
Biol.Unit 4 (28 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 HUMAN GALECTIN-9 N-TERMINAL CRD IN COMPLEX WITH N-ACETYLLACTOSAMINE TRIMER (CRYSTAL 1)
Authors
:
M. Nagae, N. Nishi, T. Murata, T. Usui, T. Nakamura, S. Wakatsuki, R. Kat
Date
:
06 Feb 08 (Deposition) - 30 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.84
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Beta Sandwich, Carbohydrate Binding Protein, Galectin, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Nagae, N. Nishi, T. Murata, T. Usui, T. Nakamura, S. Wakatsuki, R. Kato
Structural Analysis Of The Recognition Mechanism Of Poly-N-Acetyllactosamine By The Human Galectin-9 N-Terminal Carbohydrate Recognition Domain.
Glycobiology V. 19 112 2009
[
close entry info
]
Hetero Components
(3, 23)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
1e: BETA-D-GALACTOSE (GALe)
1f: BETA-D-GALACTOSE (GALf)
1g: BETA-D-GALACTOSE (GALg)
1h: BETA-D-GALACTOSE (GALh)
1i: BETA-D-GALACTOSE (GALi)
1j: BETA-D-GALACTOSE (GALj)
1k: BETA-D-GALACTOSE (GALk)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3a: (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ET... (RPNa)
3b: (R)-1-PARA-NITRO-PHENYL-2-AZIDO-ET... (RPNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
11
Ligand/Ion
BETA-D-GALACTOSE
2
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
RPN
2
Ligand/Ion
(R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL
[
close Hetero Component info
]
Sites
(22, 22)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC9 (SOFTWARE)
18: CC1 (SOFTWARE)
19: CC2 (SOFTWARE)
20: CC3 (SOFTWARE)
21: CC4 (SOFTWARE)
22: CC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:53 , SER A:54 , GLY B:69
BINDING SITE FOR RESIDUE NAG A 1002
02
AC2
SOFTWARE
GLN B:94 , LYS B:95
BINDING SITE FOR RESIDUE GAL A 1003
03
AC3
SOFTWARE
ARG A:44 , ASN A:48 , HIS A:61 , ASN A:137
BINDING SITE FOR RESIDUE NAG A 1004
04
AC4
SOFTWARE
ASN A:137
BINDING SITE FOR RESIDUE GAL A 1005
05
AC5
SOFTWARE
HIS A:61 , ASN A:63 , ARG A:65 , ASN A:75 , GLU A:85
BINDING SITE FOR RESIDUE GAL A 1006
06
AC6
SOFTWARE
GLN A:30 , ARG A:65 , GLU A:85 , ARG A:87 , PHE A:123
BINDING SITE FOR RESIDUE NAG A 1007
07
AC7
SOFTWARE
PRO B:16 , SER B:18 , PHE B:53 , SER B:54
BINDING SITE FOR RESIDUE NAG B 1009
08
AC8
SOFTWARE
SER B:18 , PHE B:53
BINDING SITE FOR RESIDUE GAL B 1010
09
AC9
SOFTWARE
ARG B:44 , ASN B:48 , HIS B:61 , ASN B:137
BINDING SITE FOR RESIDUE NAG B 1011
10
BC1
SOFTWARE
SER B:54 , ASN B:137
BINDING SITE FOR RESIDUE GAL B 1012
11
BC2
SOFTWARE
HIS B:61 , ASN B:63 , ARG B:65 , ASN B:75 , TRP B:82 , GLU B:85
BINDING SITE FOR RESIDUE GAL B 1013
12
BC3
SOFTWARE
GLN B:30 , ARG B:65 , GLU B:85 , ARG B:87 , PHE B:123
BINDING SITE FOR RESIDUE NAG B 1014
13
BC4
SOFTWARE
ASN C:48 , HIS C:61 , ASN C:137 , GLN D:26 , ASP D:27
BINDING SITE FOR RESIDUE NAG C 1015
14
BC5
SOFTWARE
ASN C:137
BINDING SITE FOR RESIDUE GAL C 1016
15
BC6
SOFTWARE
HIS C:61 , ASN C:63 , ARG C:65 , ASN C:75 , TRP C:82 , GLU C:85 , ASP D:27
BINDING SITE FOR RESIDUE GAL C 1017
16
BC7
SOFTWARE
ARG C:65 , TRP C:82 , GLU C:85 , ARG C:87 , ASP D:27
BINDING SITE FOR RESIDUE NAG C 1018
17
BC9
SOFTWARE
GLN C:26 , ASN D:48 , HIS D:61 , TRP D:82 , ASN D:137
BINDING SITE FOR RESIDUE NAG D 1020
18
CC1
SOFTWARE
GLY D:55 , ASN D:137
BINDING SITE FOR RESIDUE GAL D 1021
19
CC2
SOFTWARE
HIS D:61 , ASN D:63 , ARG D:65 , ASN D:75 , TRP D:82 , GLU D:85
BINDING SITE FOR RESIDUE GAL D 1022
20
CC3
SOFTWARE
ARG D:65 , TRP D:82 , GLU D:85 , ARG D:87
BINDING SITE FOR RESIDUE NAG D 1023
21
CC4
SOFTWARE
GLN A:30 , LEU A:104 , LYS A:111 , MET A:113 , LEU A:118
BINDING SITE FOR RESIDUE RPN A 1001
22
CC5
SOFTWARE
GLN B:30 , LEU B:104 , LYS B:111 , MET B:113 , LEU B:118
BINDING SITE FOR RESIDUE RPN B 1008
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: GALECTIN (A:17-148,B:17-148,C:17-148,D:17-14...)
;
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.
LEG9_HUMAN
17-148
227-355
4
A:17-148
B:17-148
C:17-148
D:17-147
-
[
close PROSITE info
]
Exons
(4, 16)
Info
All Exons
Exon 1.1a (A:6-13 | B:7-13 | C:7-13 | D:7-13)
Exon 1.2 (A:14-44 | B:14-44 | C:14-44 | D:14...)
Exon 1.3a (A:44-111 | B:44-111 | C:44-111 | D...)
Exon 1.5 (A:112-148 | B:112-148 | C:112-148 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3a
4: Boundary 1.3a/1.5
5: Boundary 1.5/1.6
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
ENST00000395473
1a
ENSE00002165006
chr17:
25956824-25958330
1507
LEG9_HUMAN
1-13
13
4
A:6-13
B:7-13
C:7-13
D:7-13
8
7
7
7
1.2
ENST00000395473
2
ENSE00001721697
chr17:
25965289-25965380
92
LEG9_HUMAN
14-44
31
4
A:14-44
B:14-44
C:14-44
D:14-44
31
31
31
31
1.3a
ENST00000395473
3a
ENSE00001630948
chr17:
25967598-25967799
202
LEG9_HUMAN
44-111
68
4
A:44-111
B:44-111
C:44-111
D:44-111
68
68
68
68
1.5
ENST00000395473
5
ENSE00001709088
chr17:
25969264-25969374
111
LEG9_HUMAN
112-148
37
4
A:112-148
B:112-148
C:112-148
D:112-147
37
37
37
36
1.6
ENST00000395473
6
ENSE00001727464
chr17:
25970551-25970646
96
LEG9_HUMAN
149-180
32
0
-
-
1.7c
ENST00000395473
7c
ENSE00001611626
chr17:
25972340-25972375
36
LEG9_HUMAN
181-192
12
0
-
-
1.7d
ENST00000395473
7d
ENSE00001697897
chr17:
25972887-25972937
51
LEG9_HUMAN
193-209
17
0
-
-
1.8
ENST00000395473
8
ENSE00001698891
chr17:
25973573-25973614
42
LEG9_HUMAN
210-223
14
0
-
-
1.9a
ENST00000395473
9a
ENSE00001597519
chr17:
25974056-25974144
89
LEG9_HUMAN
224-253
30
0
-
-
1.9c
ENST00000395473
9c
ENSE00001271333
chr17:
25974296-25974458
163
LEG9_HUMAN
253-307
55
0
-
-
1.10f
ENST00000395473
10f
ENSE00001859656
chr17:
25975862-25976586
725
LEG9_HUMAN
308-355
48
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2zhma_ (A:)
1b: SCOP_d2zhmb_ (B:)
1c: SCOP_d2zhmc_ (C:)
1d: SCOP_d2zhmd_ (D:)
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
d2zhma_
A:
1b
d2zhmb_
B:
1c
d2zhmc_
C:
1d
d2zhmd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Gal_bind_lectin_2zhmD01 (D:16-147)
1b: PFAM_Gal_bind_lectin_2zhmD02 (D:16-147)
1c: PFAM_Gal_bind_lectin_2zhmD03 (D:16-147)
1d: PFAM_Gal_bind_lectin_2zhmD04 (D:16-147)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Gal-bind_lectin
(60)
Homo sapiens (Human)
(25)
1a
Gal-bind_lectin-2zhmD01
D:16-147
1b
Gal-bind_lectin-2zhmD02
D:16-147
1c
Gal-bind_lectin-2zhmD03
D:16-147
1d
Gal-bind_lectin-2zhmD04
D:16-147
[
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
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 (113 KB)
Header - Asym.Unit
Biol.Unit 1 (30 KB)
Header - Biol.Unit 1
Biol.Unit 2 (30 KB)
Header - Biol.Unit 2
Biol.Unit 3 (29 KB)
Header - Biol.Unit 3
Biol.Unit 4 (28 KB)
Header - Biol.Unit 4
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
2ZHM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help