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.
5J5J
Asym. Unit
Info
Asym.Unit (195 KB)
Biol.Unit 1 (184 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 A CHIMERA OF HUMAN DESMOCOLLIN-2 EC1 AND HUMAN DESMOGLEIN-2 EC2-EC5
Authors
:
J. Brasch, O. J. Harrison, L. Shapiro
Date
:
02 Apr 16 (Deposition) - 22 Jun 16 (Release) - 13 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.29
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Extracellular Cadherin Domain, Cell Adhesion, Desmosome, Cell Surface
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
O. J. Harrison, J. Brasch, G. Lasso, P. S. Katsamba, G. Ahlsen, B. Honig L. Shapiro
Structural Basis Of Adhesive Binding By Desmocollins And Desmogleins.
Proc. Natl. Acad. Sci. Usa V. 113 7160 2016
[
close entry info
]
Hetero Components
(7, 34)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
2k: CALCIUM ION (CAk)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
4a: ALPHA-L-FUCOSE (FUCa)
5a: BETA-D-GALACTOSE (GALa)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
6d: ALPHA-D-MANNOSE (MANd)
6e: ALPHA-D-MANNOSE (MANe)
6f: ALPHA-D-MANNOSE (MANf)
6g: ALPHA-D-MANNOSE (MANg)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
7i: N-ACETYL-D-GLUCOSAMINE (NAGi)
7j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
CA
11
Ligand/Ion
CALCIUM ION
3
CL
2
Ligand/Ion
CHLORIDE ION
4
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
5
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
6
MAN
7
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(21, 21)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:233 , ARG A:427 , THR A:429
binding site for residue MAN A 609
02
AC2
SOFTWARE
LYS A:417 , THR A:429 , THR A:431
binding site for residue MAN A 610
03
AC3
SOFTWARE
SER A:340 , LYS A:417 , THR A:433
binding site for residue MAN A 611
04
AC4
SOFTWARE
ASN A:411
binding site for residue NAG A 620
05
AC5
SOFTWARE
LYS A:129 , ASN A:131 , HOH A:705
binding site for residue NAG A 621
06
AC6
SOFTWARE
GLU A:11 , ASP A:67 , GLU A:69 , ASP A:103
binding site for residue CA A 622
07
AC7
SOFTWARE
GLU A:11 , GLU A:69 , ASP A:100 , ILE A:101 , ASP A:103 , ASP A:136
binding site for residue CA A 623
08
AC8
SOFTWARE
ASN A:102 , ASN A:104 , ASP A:134 , ASP A:136 , ASN A:142 , ASP A:192
binding site for residue CA A 624
09
AC9
SOFTWARE
GLU A:119 , ASP A:177 , GLU A:179 , ASP A:216
binding site for residue CA A 625
10
AD1
SOFTWARE
GLU A:119 , GLU A:179 , ASP A:213 , VAL A:214 , ASP A:216 , ASP A:248
binding site for residue CA A 626
11
AD2
SOFTWARE
ASN A:215 , ASN A:217 , ASP A:246 , ASP A:248 , ASN A:254 , ASN A:305
binding site for residue CA A 627
12
AD3
SOFTWARE
GLU A:232 , GLU A:292 , ASN A:330 , VAL A:331 , GLU A:333 , ASP A:368
binding site for residue CA A 628
13
AD4
SOFTWARE
GLU A:232 , ASP A:290 , GLU A:292 , GLU A:333 , GLU A:367
binding site for residue CA A 629
14
AD5
SOFTWARE
GLU A:348 , GLU A:405 , ASP A:440 , ILE A:441 , ASP A:443 , ASP A:470
binding site for residue CA A 630
15
AD6
SOFTWARE
GLU A:348 , ASP A:403 , GLU A:405 , ASP A:443 , ASN A:444
binding site for residue CA A 631
16
AD7
SOFTWARE
ASN A:442 , ASN A:444 , ASP A:468 , ASP A:470 , ASN A:474 , ASP A:523
binding site for residue CA A 632
17
AD8
SOFTWARE
LYS A:318
binding site for residue CL A 633
18
AD9
SOFTWARE
SER A:479 , PHE A:480 , GLN A:498
binding site for residue CL A 634
19
AE1
SOFTWARE
ASN A:31 , ARG A:191 , THR A:198 , ASP A:199 , LYS A:200 , GLN A:204
binding site for Poly-Saccharide residues NAG A 601 through GAL A 608 bound to ASN A 31
20
AE2
SOFTWARE
ASN A:463 , THR A:465 , GLU A:499 , SER A:502
binding site for Poly-Saccharide residues NAG A 612 through MAN A 617
21
AE3
SOFTWARE
ASN A:258 , PHE A:259 , THR A:260 , ASN A:305 , LYS A:306 , ASN A:463 , THR A:465 , GLU A:499 , SER A:502 , FUC A:614
binding site for Poly-Saccharide residues NAG A 618 through NAG A 619
[
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
(0, 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.
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
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 (195 KB)
Header - Asym.Unit
Biol.Unit 1 (184 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
5J5J
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help