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.
3OED
Biol. Unit 1
Info
Asym.Unit (280 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (139 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF THE COMPLEX BETWEEN COMPLEMENT RECEPTOR CR2 AND ITS LIGAND COMPLEMENT FRAGMENT C3D
Authors
:
D. E. Isenman, J. M. H. Van Den Elsen
Date
:
12 Aug 10 (Deposition) - 11 May 11 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.16
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Complement Receptor, Complement Fragment C3D, B Cell, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Van Den Elsen, D. E. Isenman
A Crystal Structure Of The Complex Between Human Complement Receptor 2 And Its Ligand C3D.
Science V. 332 608 2011
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(7, 7)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_063655 (R49L, chain A, )
2: VAR_063216 (A101V, chain A, )
3: VAR_063217 (D122N, chain A, )
4: VAR_063218 (C165W, chain A, )
5: VAR_063219 (Q168K, chain A, )
6: VAR_022761 (D223N, chain A, )
7: VAR_019207 (G231D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_063655
R
1042
L
CO3_HUMAN
Disease (AHUS5)
---
A
R
49
L
2
UniProt
VAR_063216
A
1094
V
CO3_HUMAN
Disease (AHUS5)
---
A
A
101
V
3
UniProt
VAR_063217
D
1115
N
CO3_HUMAN
Disease (AHUS5)
---
A
D
122
N
4
UniProt
VAR_063218
C
1158
W
CO3_HUMAN
Disease (AHUS5)
---
A
C
165
W
5
UniProt
VAR_063219
Q
1161
K
CO3_HUMAN
Disease (AHUS5)
---
A
Q
168
K
6
UniProt
VAR_022761
D
1216
N
CO3_HUMAN
Unclassified
---
A
D
223
N
7
UniProt
VAR_019207
G
1224
D
CO3_HUMAN
Polymorphism
11569534
A
G
231
D
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 3)
Info
All PROSITE Patterns/Profiles
1: SUSHI (C:1-64)
2: ALPHA_2_MACROGLOBULIN (A:14-22)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
CR2_HUMAN
21-84
89-148
152-212
213-273
274-344
408-468
349-407
469-524
525-595
600-659
660-716
717-781
786-845
849-909
910-970
2
C:1-64
-
C:69-128
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
ALPHA_2_MACROGLOBULIN
PS00477
Alpha-2-macroglobulin family thiolester region signature.
CO3_HUMAN
1007-1015
1
A:14-22
-
[
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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3oeda_ (A:)
1b: SCOP_d3oedb_ (B:)
2a: SCOP_d3oedc1 (C:0-65)
2b: SCOP_d3oedc2 (C:66-129)
2c: SCOP_d3oedd1 (D:0-65)
2d: SCOP_d3oedd2 (D:66-129)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
alpha/alpha toroid
(324)
Superfamily
:
Terpenoid cyclases/Protein prenyltransferases
(151)
Family
:
Complement components
(19)
Protein domain
:
Thio-ester containing domain (TED) from Complement C3, aka C3d or C3dg
(16)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3oeda_
A:
1b
d3oedb_
B:
Class
:
Small proteins
(3458)
Fold
:
Complement control module/SCR domain
(70)
Superfamily
:
Complement control module/SCR domain
(70)
Family
:
Complement control module/SCR domain
(67)
Protein domain
:
automated matches
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3oedc1
C:0-65
2b
d3oedc2
C:66-129
2c
d3oedd1
D:0-65
2d
d3oedd2
D:66-129
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_A2M_comp_3oedB01 (B:58-291)
1b: PFAM_A2M_comp_3oedB02 (B:58-291)
2a: PFAM_Sushi_3oedD01 (D:71-126)
2b: PFAM_Sushi_3oedD02 (D:71-126)
2c: PFAM_Sushi_3oedD03 (D:71-126)
2d: PFAM_Sushi_3oedD04 (D:71-126)
3a: PFAM_Thiol_ester_cl_3oedB03 (B:6-36)
3b: PFAM_Thiol_ester_cl_3oedB04 (B:6-36)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
A2M_comp
(16)
Homo sapiens (Human)
(13)
1a
A2M_comp-3oedB01
B:58-291
1b
A2M_comp-3oedB02
B:58-291
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
2a
Sushi-3oedD01
D:71-126
2b
Sushi-3oedD02
D:71-126
2c
Sushi-3oedD03
D:71-126
2d
Sushi-3oedD04
D:71-126
Clan
:
no clan defined [family: Thiol-ester_cl]
(12)
Family
:
Thiol-ester_cl
(12)
Homo sapiens (Human)
(9)
3a
Thiol-ester_cl-3oedB03
B:6-36
3b
Thiol-ester_cl-3oedB04
B:6-36
[
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 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 (280 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (139 KB)
Header - Biol.Unit 2
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
3OED
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help