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.
PLEASE WAIT...
Getting 'Exon' information from database.
1MGX
Asym. Unit
Info
Asym.Unit (23 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(7 )
Title
:
COAGULATION FACTOR, MG(II), NMR, 7 STRUCTURES (BACKBONE ATOMS ONLY)
Authors
:
S. J. Freedman, B. C. Furie, B. Furie, J. D. Baleja
Date
:
21 Jun 95 (Deposition) - 08 Nov 96 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (7 x)
Keywords
:
Coagulation Factor, Signal, Plasma
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. J. Freedman, M. D. Blostein, J. D. Baleja, M. Jacobs, B. C. Furie, B. Furie
Identification Of The Phospholipid Binding Site In The Vitamin K-Dependent Blood Coagulation Protein Factor Ix.
J. Biol. Chem. V. 271 16227 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 12)
Info
All Hetero Components
1a: GAMMA-CARBOXY-GLUTAMIC ACID (CGUa)
1b: GAMMA-CARBOXY-GLUTAMIC ACID (CGUb)
1c: GAMMA-CARBOXY-GLUTAMIC ACID (CGUc)
1d: GAMMA-CARBOXY-GLUTAMIC ACID (CGUd)
1e: GAMMA-CARBOXY-GLUTAMIC ACID (CGUe)
1f: GAMMA-CARBOXY-GLUTAMIC ACID (CGUf)
1g: GAMMA-CARBOXY-GLUTAMIC ACID (CGUg)
1h: GAMMA-CARBOXY-GLUTAMIC ACID (CGUh)
1i: GAMMA-CARBOXY-GLUTAMIC ACID (CGUi)
1j: GAMMA-CARBOXY-GLUTAMIC ACID (CGUj)
1k: GAMMA-CARBOXY-GLUTAMIC ACID (CGUk)
1l: GAMMA-CARBOXY-GLUTAMIC ACID (CGUl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
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
(18, 18)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
01: VAR_006530 (N2I, chain A, )
02: VAR_006531 (S3P, chain A, )
03: VAR_017344 (L6S, chain A, )
04: VAR_006532 (E7A, chain A, )
05: VAR_006533 (E8G, chain A, )
06: VAR_006534 (F9C, chain A, )
07: VAR_006535 (G12A, chain A, )
08: VAR_006536 (G12R, chain A, )
09: VAR_006538 (E20V, chain A, )
10: VAR_006539 (E21K, chain A, )
11: VAR_006540 (F25S, chain A, )
12: VAR_006541 (E27K, chain A, )
13: VAR_006542 (E27V, chain A, )
14: VAR_017308 (R29Q, chain A, )
15: VAR_017309 (E33D, chain A, )
16: VAR_017345 (T38R, chain A, )
17: VAR_006543 (Y45C, chain A, )
18: VAR_006544 (D47G, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006530
N
48
I
FA9_HUMAN
Disease (HEMB)
---
A
N
2
I
02
UniProt
VAR_006531
S
49
P
FA9_HUMAN
Disease (HEMB)
---
A
S
3
P
03
UniProt
VAR_017344
L
52
S
FA9_HUMAN
Disease (HEMB)
---
A
L
6
S
04
UniProt
VAR_006532
E
53
A
FA9_HUMAN
Disease (HEMB)
---
A
E
7
A
05
UniProt
VAR_006533
E
54
G
FA9_HUMAN
Disease (HEMB)
---
A
E
8
G
06
UniProt
VAR_006534
F
55
C
FA9_HUMAN
Disease (HEMB)
---
A
F
9
C
07
UniProt
VAR_006535
G
58
A
FA9_HUMAN
Disease (HEMB)
---
A
G
12
A
08
UniProt
VAR_006536
G
58
R
FA9_HUMAN
Disease (HEMB)
---
A
G
12
R
09
UniProt
VAR_006538
E
66
V
FA9_HUMAN
Disease (HEMB)
---
A
E
20
V
10
UniProt
VAR_006539
E
67
K
FA9_HUMAN
Disease (HEMB)
---
A
E
21
K
11
UniProt
VAR_006540
F
71
S
FA9_HUMAN
Disease (HEMB)
---
A
F
25
S
12
UniProt
VAR_006541
E
73
K
FA9_HUMAN
Disease (HEMB)
---
A
E
27
K
13
UniProt
VAR_006542
E
73
V
FA9_HUMAN
Disease (HEMB)
---
A
E
27
V
14
UniProt
VAR_017308
R
75
Q
FA9_HUMAN
Disease (HEMB)
---
A
R
29
Q
15
UniProt
VAR_017309
E
79
D
FA9_HUMAN
Disease (HEMB)
---
A
E
33
D
16
UniProt
VAR_017345
T
84
R
FA9_HUMAN
Disease (HEMB)
---
A
T
38
R
17
UniProt
VAR_006543
Y
91
C
FA9_HUMAN
Disease (HEMB)
---
A
Y
45
C
18
UniProt
VAR_006544
D
93
G
FA9_HUMAN
Disease (HEMB)
---
A
D
47
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 3)
Info
All PROSITE Patterns/Profiles
1: GLA_2 (A:1-47)
2: GLA_1 (A:17-42)
3: EGF_3 (A:47-47)
4: EGF_CA (A:47-47)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GLA_2
PS50998
Gla domain profile.
FA9_HUMAN
47-93
1
A:1-47
2
GLA_1
PS00011
Vitamin K-dependent carboxylation domain.
FA9_HUMAN
63-88
1
A:17-42
3
EGF_3
PS50026
EGF-like domain profile.
FA9_HUMAN
93-129
1
A:47-47
4
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
FA9_HUMAN
93-117
1
A:47-47
[
close PROSITE info
]
Exons
(3, 3)
Info
All Exons
Exon 1.2b (A:1-38)
Exon 1.3 (A:39-47)
Exon 1.4a (A:47-47)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1b/1.2b
2: Boundary 1.2b/1.3
3: Boundary 1.3/1.4a
4: Boundary 1.4a/1.5b
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
1.1b
ENST00000218099
1b
ENSE00002195519
X:138612917-138613011
95
FA9_HUMAN
1-30
30
0
-
-
1.2b
ENST00000218099
2b
ENSE00000677287
X:138619169-138619332
164
FA9_HUMAN
30-84
55
1
A:1-38
38
1.3
ENST00000218099
3
ENSE00001173335
X:138619521-138619545
25
FA9_HUMAN
85-93
9
1
A:39-47
9
1.4a
ENST00000218099
4a
ENSE00001173327
X:138623235-138623348
114
FA9_HUMAN
93-131
39
1
A:47-47
1
1.5b
ENST00000218099
5b
ENSE00001173320
X:138630522-138630650
129
FA9_HUMAN
131-174
44
0
-
-
1.6
ENST00000218099
6
ENSE00001173315
X:138633221-138633423
203
FA9_HUMAN
174-241
68
0
-
-
1.7
ENST00000218099
7
ENSE00001173311
X:138642900-138643014
115
FA9_HUMAN
242-280
39
0
-
-
1.8b
ENST00000218099
8b
ENSE00001029145
X:138643683-138645617
1935
FA9_HUMAN
280-461
182
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1mgxa_ (A:)
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 IX (IXa)
(7)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1mgxa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1mgxA00 (A:1-47)
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)
Human (Homo sapiens)
(5)
1a
1mgxA00
A:1-47
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Gla_1mgxA01 (A:6-47)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Gla]
(24)
Family
:
Gla
(24)
Homo sapiens (Human)
(14)
1a
Gla-1mgxA01
A:6-47
[
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 (23 KB)
Header - Asym.Unit
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
1MGX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
