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.
4R9J
Biol. Unit 1
Info
Asym.Unit (230 KB)
Biol.Unit 1 (222 KB)
Biol.Unit 2 (76 KB)
Biol.Unit 3 (76 KB)
Biol.Unit 4 (78 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
L-FICOLIN COMPLEXED TO GLUCOSAMINE-6-SULFATE
Authors
:
E. Laffly, M. Lacroix, L. Martin, E. Vassal-Stermann, N. Thielens, C. G
Date
:
05 Sep 14 (Deposition) - 05 Nov 14 (Release) - 14 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,G
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: B (1x)
Biol. Unit 4: G (1x)
Keywords
:
Fibrinogen-Like Domain, Innate Immunity, Pattern Recognition Protein, Lectin, Immunology, Lectin-Like, Sugar Binding Protein, Plasma, Extracellular
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Laffly, M. Lacroix, L. Martin, E. Vassal-Stermann, N. M. Thielens, C. Gaboriaud
Human Ficolin-2 Recognition Versatility Extended: An Update On The Binding Of Ficolin-2 To Sulfated/Phosphated Carbohydrates.
Febs Lett. V. 588 4694 2014
[
close entry info
]
Hetero Components
(5, 15)
Info
All Hetero Components
1a: 2-AMINO-2-DEOXY-6-O-SULFO-ALPHA-D-... (3LJa)
1b: 2-AMINO-2-DEOXY-6-O-SULFO-ALPHA-D-... (3LJb)
1c: 2-AMINO-2-DEOXY-6-O-SULFO-ALPHA-D-... (3LJc)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
2e: ACETATE ION (ACTe)
2f: ACETATE ION (ACTf)
2g: ACETATE ION (ACTg)
3a: BETA-D-MANNOSE (BMAa)
4a: CALCIUM ION (CAa)
4b: CALCIUM ION (CAb)
4c: CALCIUM ION (CAc)
4d: CALCIUM ION (CAd)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3LJ
3
Ligand/Ion
2-AMINO-2-DEOXY-6-O-SULFO-ALPHA-D-GLUCOPYRANOSE
2
ACT
7
Ligand/Ion
ACETATE ION
3
BMA
1
Ligand/Ion
BETA-D-MANNOSE
4
CA
-1
Ligand/Ion
CALCIUM ION
5
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP G:224 , ASP G:226 , ASN G:228 , GLY G:230 , HOH G:401 , HOH G:402
BINDING SITE FOR RESIDUE CA G 301
02
AC2
SOFTWARE
HOH A:415 , PHE G:236 , CYS G:245 , HIS G:246 , HOH G:415
BINDING SITE FOR RESIDUE ACT G 302
03
AC3
SOFTWARE
GLY A:92 , TRP A:93 , ACT B:301 , ARG G:144
BINDING SITE FOR RESIDUE ACT G 303
04
AC4
SOFTWARE
ASP G:208 , LEU G:210 , THR G:211 , PHE G:212 , HOH G:466
BINDING SITE FOR RESIDUE ACT G 304
05
AC5
SOFTWARE
ARG G:132 , ASP G:133 , THR G:136 , LYS G:221
BINDING SITE FOR RESIDUE SO4 G 305
06
AC6
SOFTWARE
ASP A:224 , ASP A:226 , ASN A:228 , GLY A:230 , HOH A:405 , HOH A:417
BINDING SITE FOR RESIDUE CA A 301
07
AC7
SOFTWARE
CYS A:245 , HIS A:246 , BMA G:308
BINDING SITE FOR RESIDUE ACT A 302
08
AC8
SOFTWARE
GLU A:203 , GLY A:204 , SER A:205 , GLY B:207 , ASP B:208
BINDING SITE FOR RESIDUE ACT A 303
09
AC9
SOFTWARE
ASP A:222 , HOH A:425 , HOH A:426 , HOH A:427
BINDING SITE FOR RESIDUE CA A 304
10
BC1
SOFTWARE
ARG A:132 , ASP A:133 , THR A:136 , LYS A:221 , HOH A:428 , HOH A:437 , HOH A:474
BINDING SITE FOR RESIDUE 3LJ A 305
11
BC2
SOFTWARE
ARG A:144 , GLY B:92 , TRP B:93 , ACT G:303
BINDING SITE FOR RESIDUE ACT B 301
12
BC3
SOFTWARE
ASP B:224 , ASP B:226 , ASN B:228 , GLY B:230 , HOH B:437 , HOH B:444
BINDING SITE FOR RESIDUE CA B 302
13
BC4
SOFTWARE
CYS B:245 , HIS B:246
BINDING SITE FOR RESIDUE ACT B 303
14
BC5
SOFTWARE
ARG B:132 , ASP B:133 , THR B:136 , LYS B:221 , HOH B:434 , GLY G:114
BINDING SITE FOR RESIDUE 3LJ B 304
15
BC6
SOFTWARE
LYS A:269 , GLY A:271 , LYS A:272 , GLY A:273 , ARG B:183 , SER B:184 , GLY B:199 , ALA B:200 , HOH B:432
BINDING SITE FOR RESIDUE 3LJ B 305
16
BC7
SOFTWARE
ASN A:215
BINDING SITE FOR MONO-SACCHARIDE NAG A 306 BOUND TO ASN A 215
17
BC8
SOFTWARE
GLY A:260 , PHE A:262 , ASN A:275 , ACT A:302 , ASN G:215 , HOH G:427 , HOH G:455
BINDING SITE FOR CHAIN G OF SUGAR BOUND TO ASN G 215 RESIDUES 306 TO 308
[
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 A
Chain B
Chain G
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 (230 KB)
Header - Asym.Unit
Biol.Unit 1 (222 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 KB)
Header - Biol.Unit 2
Biol.Unit 3 (76 KB)
Header - Biol.Unit 3
Biol.Unit 4 (78 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
4R9J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help