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.
2W94
Asym. Unit
Info
Asym.Unit (147 KB)
Biol.Unit 1 (141 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT 1.8 ANGSTROM RESOLUTION
Authors
:
K. Saboia Aragao, A. Imberty, A. Varrot
Date
:
21 Jan 09 (Deposition) - 31 Mar 10 (Release) - 21 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Cell Adhesion, H Type Lectin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Mathieu, K. Saboia Aragao, A. Imberty, A. Varrot
Discoidin I From Dictyostelium Discoideum And Interactions With Oligosaccharides: Specificity, Affinity, Crystal Structures And Comparison With Discoidin Ii.
J. Mol. Biol. V. 400 540 2010
[
close entry info
]
Hetero Components
(5, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
2c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
3b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
4a: NICKEL (II) ION (NIa)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM ION
2
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
3
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
4
NI
1
Ligand/Ion
NICKEL (II) ION
5
SO4
4
Ligand/Ion
SULFATE 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
VAL A:62 , ARG A:92 , TRP A:100 , HOH A:2345 , HOH A:2346 , ASN C:12
BINDING SITE FOR RESIDUE MPD A1254
02
AC2
SOFTWARE
ARG A:79 , GLN A:84 , HIS A:142 , HOH A:2047 , THR B:41 , HOH B:2075
BINDING SITE FOR RESIDUE MPD A1255
03
AC3
SOFTWARE
ARG A:104 , VAL A:109 , THR A:110 , HIS A:121 , HOH A:2347
BINDING SITE FOR RESIDUE SO4 A1256
04
AC4
SOFTWARE
ASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2281 , HOH B:2282
BINDING SITE FOR RESIDUE CA A1257
05
AC5
SOFTWARE
HIS A:16 , HIS B:16 , HIS C:16 , HOH C:2035
BINDING SITE FOR RESIDUE NI A1258
06
AC6
SOFTWARE
SER A:157 , VAL A:158 , THR A:159 , SER B:157 , THR B:159 , SER C:157 , THR C:159
BINDING SITE FOR RESIDUE SO4 A1259
07
AC7
SOFTWARE
THR A:41 , TYR B:23 , ARG B:79 , GLN B:84 , HIS B:142 , HOH B:2042
BINDING SITE FOR RESIDUE MPD B1254
08
AC8
SOFTWARE
ARG B:104 , VAL B:109 , THR B:110 , HIS B:121
BINDING SITE FOR RESIDUE SO4 B1255
09
AC9
SOFTWARE
ASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2263 , HOH C:2264
BINDING SITE FOR RESIDUE CA B1256
10
BC1
SOFTWARE
ARG C:18 , VAL C:62 , ARG C:92 , TRP C:100 , HIS C:135 , HOH C:2305
BINDING SITE FOR RESIDUE MRD C1254
11
BC2
SOFTWARE
THR C:41 , ASN C:42 , ARG C:79 , GLN C:84 , HIS C:142 , HOH C:2075
BINDING SITE FOR RESIDUE MRD C1255
12
BC3
SOFTWARE
ARG C:104 , VAL C:109 , THR C:110 , HIS C:121 , HOH C:2165 , HOH C:2306
BINDING SITE FOR RESIDUE SO4 C1256
13
BC4
SOFTWARE
GLN A:219 , HOH A:2288 , HOH A:2289 , ASP C:164 , ASP C:203 , ASP C:246
BINDING SITE FOR RESIDUE CA C1257
[
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, 6)
Info
All PROSITE Patterns/Profiles
1: FA58C_3 (A:1-152,B:1-152,C:1-152)
2: FA58C_1 (A:49-78,B:49-78,C:49-78)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FA58C_3
PS50022
Coagulation factors 5/8 type C domain (FA58C) profile.
DIS1A_DICDI
1-152
3
A:1-152
B:1-152
C:1-152
2
FA58C_1
PS01285
Coagulation factors 5/8 type C domain (FA58C) signature 1.
DIS1A_DICDI
49-78
3
A:49-78
B:49-78
C:49-78
[
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
(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
(2, 6)
Info
all PFAM domains
1a: PFAM_F5_F8_type_C_2w94C01 (C:16-149)
1b: PFAM_F5_F8_type_C_2w94C02 (C:16-149)
1c: PFAM_F5_F8_type_C_2w94C03 (C:16-149)
2a: PFAM_H_lectin_2w94C04 (C:180-252)
2b: PFAM_H_lectin_2w94C05 (C:180-252)
2c: PFAM_H_lectin_2w94C06 (C:180-252)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GBD
(153)
Family
:
F5_F8_type_C
(45)
Dictyostelium discoideum (Slime mold)
(8)
1a
F5_F8_type_C-2w94C01
C:16-149
1b
F5_F8_type_C-2w94C02
C:16-149
1c
F5_F8_type_C-2w94C03
C:16-149
Clan
:
no clan defined [family: H_lectin]
(8)
Family
:
H_lectin
(8)
Dictyostelium discoideum (Slime mold)
(8)
2a
H_lectin-2w94C04
C:180-252
2b
H_lectin-2w94C05
C:180-252
2c
H_lectin-2w94C06
C:180-252
[
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
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 (147 KB)
Header - Asym.Unit
Biol.Unit 1 (141 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
2W94
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
