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.
3ZQK
Biol. Unit 1
Info
Asym.Unit (203 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (68 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
VON WILLEBRAND FACTOR A2 DOMAIN WITH CALCIUM
Authors
:
A. J. Jakobi, E. G. Huizinga
Date
:
09 Jun 11 (Deposition) - 27 Jul 11 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Blood Clotting, Adamts-13, Force Sensor, Von Willebrand Disease, Vwa Domain, Haemostasis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Jakobi, A. Mashaghi, S. J. Tans, E. G. Huizinga
Calcium Modulates Force Sensing By The Von Willebrand Factor A2 Domain.
Nat. Commun. V. 2 385 2011
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC5 (SOFTWARE)
5: AC6 (SOFTWARE)
6: AC8 (SOFTWARE)
7: BC1 (SOFTWARE)
8: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:1498 , ASP A:1596 , ARG A:1597 , ALA A:1600 , ASN A:1602 , HOH A:2116
BINDING SITE FOR RESIDUE CA A4675
2
AC2
SOFTWARE
GLU A:1511 , ASN A:1515 , ARG A:1569 , HOH A:2028 , HOH A:2208 , HOH A:2210 , HOH A:2211
BINDING SITE FOR RESIDUE NAG A4676
3
AC3
SOFTWARE
TYR A:1544 , ASN A:1574 , HOH A:2059 , HOH A:2092 , HOH A:2093 , HOH A:2213 , HOH A:2214 , GLN B:1526 , ARG B:1527 , MET B:1528 , LYS B:1558 , ARG B:1569
BINDING SITE FOR RESIDUE NAG A4677
4
AC5
SOFTWARE
HOH A:2011 , GLU B:1511 , ASN B:1515 , HOH B:2156
BINDING SITE FOR RESIDUE NAG B4676
5
AC6
SOFTWARE
PRO A:1551 , GLU A:1554 , HOH A:2066 , TYR B:1544 , ASN B:1574 , ARG B:1575 , HOH B:2061
BINDING SITE FOR RESIDUE NAG B4677
6
AC8
SOFTWARE
ASP A:1533 , HOH A:2051 , HOH A:2052 , GLU C:1511 , ASN C:1515 , LYS C:1518 , ILE C:1568 , LEU C:1591
BINDING SITE FOR RESIDUE NAG C4676
7
BC1
SOFTWARE
GLN A:1637 , GLU A:1640 , ARG A:1641 , LEU A:1650 , HOH A:2188 , HOH A:2189 , HOH A:2199
BINDING SITE FOR RESIDUE GOL A2675
8
BC2
SOFTWARE
GLU A:1523 , PHE A:1590 , ASP A:1596 , ASN A:1602 , ASP A:1622 , ARG A:1659 , HOH A:2037 , HOH A:2111
BINDING SITE FOR RESIDUE GOL A2676
[
close Site info
]
SAPs(SNPs)/Variants
(16, 16)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_005808 (F1514C, chain A, )
02: VAR_005809 (L1540P, chain A, )
03: VAR_014630 (L1565L, chain A, )
04: VAR_036276 (Y1570C, chain A, )
05: VAR_VWF_HUMAN_CCDS8539_1_01 (Y1570C, chain A, )
06: VAR_005810 (Y1584C, chain A, )
07: VAR_005811 (R1597G, chain A, )
08: VAR_005812 (R1597Q, chain A, )
09: VAR_005813 (R1597W, chain A, )
10: VAR_005814 (V1607D, chain A, )
11: VAR_005815 (G1609R, chain A, )
12: VAR_005816 (S1613P, chain A, )
13: VAR_005817 (I1628T, chain A, )
14: VAR_005818 (E1638K, chain A, )
15: VAR_005819 (P1648S, chain A, )
16: VAR_005820 (V1665E, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_005808
F
1514
C
VWF_HUMAN
Disease (VWD2)
---
A
F
1514
C
02
UniProt
VAR_005809
L
1540
P
VWF_HUMAN
Disease (VWD2)
---
A
L
1540
P
03
UniProt
VAR_014630
V
1565
L
VWF_HUMAN
Polymorphism
1800385
A
L
1565
L
04
UniProt
VAR_036276
Y
1570
C
VWF_HUMAN
Unclassified
---
A
Y
1570
C
05
CancerSNP
VAR_VWF_HUMAN_CCDS8539_1_01
*
Y
1570
C
VWF_HUMAN
Disease (Breast cancer)
---
A
Y
1570
C
06
UniProt
VAR_005810
Y
1584
C
VWF_HUMAN
Polymorphism
1800386
A
Y
1584
C
07
UniProt
VAR_005811
R
1597
G
VWF_HUMAN
Disease (VWD2)
---
A
R
1597
G
08
UniProt
VAR_005812
R
1597
Q
VWF_HUMAN
Disease (VWD2)
---
A
R
1597
Q
09
UniProt
VAR_005813
R
1597
W
VWF_HUMAN
Disease (VWD2)
---
A
R
1597
W
10
UniProt
VAR_005814
V
1607
D
VWF_HUMAN
Disease (VWD2)
---
A
V
1607
D
11
UniProt
VAR_005815
G
1609
R
VWF_HUMAN
Disease (VWD2)
---
A
G
1609
R
12
UniProt
VAR_005816
S
1613
P
VWF_HUMAN
Disease (VWD2)
---
A
S
1613
P
13
UniProt
VAR_005817
I
1628
T
VWF_HUMAN
Disease (VWD2)
---
A
I
1628
T
14
UniProt
VAR_005818
E
1638
K
VWF_HUMAN
Disease (VWD2)
---
A
E
1638
K
15
UniProt
VAR_005819
P
1648
S
VWF_HUMAN
Disease (VWD2)
---
A
P
1648
S
16
UniProt
VAR_005820
V
1665
E
VWF_HUMAN
Disease (VWD2)
---
A
V
1665
E
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: VWFA (A:1498-1665)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
VWFA
PS50234
VWFA domain profile.
VWF_HUMAN
1498-1665
1277-1453
1691-1871
1
A:1498-1665
-
-
-
-
[
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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3zqka_ (A:)
1b: SCOP_d3zqkb_ (B:)
1c: SCOP_d3zqkc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
vWA-like
(111)
Superfamily
:
vWA-like
(111)
Family
:
automated matches
(13)
Protein domain
:
automated matches
(13)
Human (Homo sapiens) [TaxId: 9606]
(10)
1a
d3zqka_
A:
1b
d3zqkb_
B:
1c
d3zqkc_
C:
[
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 (203 KB)
Header - Asym.Unit
Biol.Unit 1 (69 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (68 KB)
Header - Biol.Unit 3
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
3ZQK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
