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.
1WHE
Asym. Unit
Info
Asym.Unit (437 KB)
Biol.Unit 1 (24 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
COAGULATION FACTOR, NMR, 20 STRUCTURES
Authors
:
M. Sunnerhagen, G. A. Olah, J. Stenflo, S. Forsen, T. Drakenberg, J. Tre
Date
:
18 Jun 96 (Deposition) - 15 May 97 (Release) - 20 Jun 12 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Biol. Unit 1: A (1x)
Keywords
:
Glycoprotein, Hydrolase, Serine Protease, Plasma, Blood Coagulation Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sunnerhagen, G. A. Olah, J. Stenflo, S. Forsen, T. Drakenberg, J. Trewhella
The Relative Orientation Of Gla And Egf Domains In Coagulation Factor X Is Altered By Ca2+ Binding To The Firs Egf Domain. A Combined Nmr-Small Angle X-Ray Scattering Study.
Biochemistry V. 35 11547 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: (3S)-3-HYDROXY-L-ASPARTIC ACID (BHDa)
2a: GAMMA-CARBOXY-GLUTAMIC ACID (CGUa)
2b: GAMMA-CARBOXY-GLUTAMIC ACID (CGUb)
2c: GAMMA-CARBOXY-GLUTAMIC ACID (CGUc)
2d: GAMMA-CARBOXY-GLUTAMIC ACID (CGUd)
2e: GAMMA-CARBOXY-GLUTAMIC ACID (CGUe)
2f: GAMMA-CARBOXY-GLUTAMIC ACID (CGUf)
2g: GAMMA-CARBOXY-GLUTAMIC ACID (CGUg)
2h: GAMMA-CARBOXY-GLUTAMIC ACID (CGUh)
2i: GAMMA-CARBOXY-GLUTAMIC ACID (CGUi)
2j: GAMMA-CARBOXY-GLUTAMIC ACID (CGUj)
2k: GAMMA-CARBOXY-GLUTAMIC ACID (CGUk)
2l: GAMMA-CARBOXY-GLUTAMIC ACID (CGUl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BHD
1
Mod. Amino Acid
(3S)-3-HYDROXY-L-ASPARTIC ACID
2
CGU
12
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
[
close Hetero Component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(6, 5)
Info
All PROSITE Patterns/Profiles
1: GLA_1 (A:16-41)
2: EGF_3 (A:46-82)
3: EGF_CA (A:46-70)
4: ASX_HYDROXYL (A:61-72)
5: EGF_1 (A:70-81)
6: EGF_2 (A:70-81|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLA_1
PS00011
Vitamin K-dependent carboxylation domain.
FA10_BOVIN
56-81
1
A:16-41
2
EGF_3
PS50026
EGF-like domain profile.
FA10_BOVIN
86-122
1
A:46-82
3
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
FA10_BOVIN
86-110
1
A:46-70
4
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
FA10_BOVIN
101-112
1
A:61-72
5
EGF_1
PS00022
EGF-like domain signature 1.
FA10_BOVIN
110-121
1
A:70-81
6
EGF_2
PS01186
EGF-like domain signature 2.
FA10_BOVIN
110-121
149-164
1
A:70-81
-
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.2 (A:1-37)
Exon 1.3 (A:38-46)
Exon 1.4 (A:46-84)
Exon 1.5 (A:84-86)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENSBTAT00000021789
1
ENSBTAE00000377900
chr12:
84664833-84664902
70
FA10_BOVIN
1-24
24
0
-
-
1.2
ENSBTAT00000021789
2
ENSBTAE00000278163
chr12:
84666990-84667150
161
FA10_BOVIN
24-77
54
1
A:1-37
37
1.3
ENSBTAT00000021789
3
ENSBTAE00000177940
chr12:
84671119-84671143
25
FA10_BOVIN
78-86
9
1
A:38-46
9
1.4
ENSBTAT00000021789
4
ENSBTAE00000177941
chr12:
84672093-84672206
114
FA10_BOVIN
86-124
39
1
A:46-84
39
1.5
ENSBTAT00000021789
5
ENSBTAE00000425962
chr12:
84673472-84673603
132
FA10_BOVIN
124-168
45
1
A:84-86
3
1.6
ENSBTAT00000021789
6
ENSBTAE00000408790
chr12:
84675374-84675615
242
FA10_BOVIN
168-248
81
0
-
-
1.7
ENSBTAT00000021789
7
ENSBTAE00000412504
chr12:
84676748-84676865
118
FA10_BOVIN
249-288
40
0
-
-
1.8
ENSBTAT00000021789
8
ENSBTAE00000414972
chr12:
84677559-84678217
659
FA10_BOVIN
288-492
205
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1whea2 (A:1-46)
2a: SCOP_d1whea1 (A:47-86)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
GLA-domain
(44)
Superfamily
:
GLA-domain
(44)
Family
:
GLA-domain
(37)
Protein domain
:
Coagulation factor X
(4)
Cow (Bos taurus) [TaxId: 9913]
(3)
1a
d1whea2
A:1-46
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Factor X, N-terminal module
(81)
Cow (Bos taurus) [TaxId: 9913]
(5)
2a
d1whea1
A:47-86
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1wheA01 (A:1-46)
2a: CATH_1wheA02 (A:47-86)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Coagulation Factor IX
(11)
Homologous Superfamily
:
Coagulation Factor IX
(11)
Cattle (Bos taurus)
(2)
1a
1wheA01
A:1-46
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Cattle (Bos taurus)
(4)
2a
1wheA02
A:47-86
[
close CATH info
]
Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_EGF_1wheA01 (A:50-80)
2a: PFAM_Gla_1wheA02 (A:5-46)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EGF
(60)
Family
:
EGF
(31)
Bos taurus (Bovine)
(2)
1a
EGF-1wheA01
A:50-80
Clan
:
no clan defined [family: Gla]
(24)
Family
:
Gla
(24)
Bos taurus (Bovine)
(8)
2a
Gla-1wheA02
A:5-46
[
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 (437 KB)
Header - Asym.Unit
Biol.Unit 1 (24 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
1WHE
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
