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.
3JTC
Asym. Unit
Info
Asym.Unit (95 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
IMPORTANCE OF MG2+ IN THE CA2+-DEPENDENT FOLDING OF THE GAMMA-CARBOXYGLUTAMIC ACID DOMAINS OF VITAMIN K-DEPENDENT CLOTTING AND ANTICLOTTING PROTEINS
Authors
:
S. P. Bajaj, K. Vadivel, S. Agah, D. Cascio, S. Krishnaswamy, C. Esmon, K. Padmanabhan
Date
:
11 Sep 09 (Deposition) - 06 Apr 11 (Release) - 03 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Gla (Gamma-Carboxyglutamic Acid) Residues, Phospholipid Binding Groove, Ca Ion Binding, Blood Clotting, Blood Coagulation, Disulfide Bond, Glycoprotein, Membrane, Receptor, Transmembrane, Cleavage On Pair Of Basic Residues, Disease Mutation, Egf-Like Domain, Gamma- Carboxyglutamic Acid, Hydrolase, Hydroxylation, Protease, Serine Protease, Thrombophilia, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Vadivel, S. Agah, A. S. Messer, D. Cascio, M. S. Bajaj, S. Krishnaswamy, C. T. Esmon, K. Padmanabhan, S. P. Bajaj
Structural And Functional Studies Of Gamma-Carboxyglutamic Acid Domains Of Factor Viia And Activated Protein C: Role O Magnesium At Physiological Calcium.
J. Mol. Biol. V. 425 1961 2013
[
close entry info
]
Hetero Components
(6, 40)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
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)
2m: GAMMA-CARBOXY-GLUTAMIC ACID (CGUm)
2n: GAMMA-CARBOXY-GLUTAMIC ACID (CGUn)
2o: GAMMA-CARBOXY-GLUTAMIC ACID (CGUo)
2p: GAMMA-CARBOXY-GLUTAMIC ACID (CGUp)
2q: GAMMA-CARBOXY-GLUTAMIC ACID (CGUq)
2r: GAMMA-CARBOXY-GLUTAMIC ACID (CGUr)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
6a: PHOSPHATIDYLETHANOLAMINE (PTYa)
6b: PHOSPHATIDYLETHANOLAMINE (PTYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
CGU
18
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
PTY
2
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
[
close Hetero Component info
]
Sites
(22, 22)
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: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:14 , ILE A:16 , GLN A:28 , ASN A:30 , HOH A:785
BINDING SITE FOR RESIDUE NAG A 603
02
AC2
SOFTWARE
ALA A:90 , PRO A:92 , ASN A:119 , HOH A:729
BINDING SITE FOR RESIDUE NAG A 604
03
AC3
SOFTWARE
ASN A:155
BINDING SITE FOR RESIDUE NDG A 605
04
AC4
SOFTWARE
LEU A:14 , ASN A:30 , HIS A:39 , LEU A:69 , TYR A:72 , GLN A:75 , PHE A:76 , ARG A:156 , THR A:157 , GLU A:160 , GLU A:163 , PHE A:164 , CYS A:169 , HOH A:700 , HOH A:701 , HOH A:702
BINDING SITE FOR RESIDUE PTY A 606
05
AC5
SOFTWARE
HIS B:12 , GLN B:28 , ASN B:30 , ALA B:31 , SER B:32 , HOH B:637 , HOH B:653 , HOH B:667 , HOH B:722
BINDING SITE FOR RESIDUE NAG B 600
06
AC6
SOFTWARE
ALA B:90 , PRO B:92 , ASN B:119 , HOH B:626 , HOH B:701
BINDING SITE FOR RESIDUE NAG B 601
07
AC7
SOFTWARE
ASN B:155 , HOH B:660 , HOH B:686
BINDING SITE FOR RESIDUE NAG B 602
08
AC8
SOFTWARE
LEU B:11 , ASN B:30 , HIS B:39 , LEU B:69 , TYR B:72 , ARG B:156 , THR B:157 , GLU B:160 , GLU B:163 , PHE B:164 , CYS B:169 , HOH B:638 , HOH B:642 , HOH B:679 , HOH B:714
BINDING SITE FOR RESIDUE PTY B 607
09
AC9
SOFTWARE
GLU A:86 , HOH A:615 , CGU C:25 , CGU C:29
BINDING SITE FOR RESIDUE MG C 34
10
BC1
SOFTWARE
GLU A:86 , CGU C:7 , CGU C:26 , CGU C:29 , HOH C:47
BINDING SITE FOR RESIDUE CA C 35
11
BC2
SOFTWARE
CGU C:7 , CGU C:16 , CGU C:26 , CGU C:29 , HOH C:56 , HOH C:57 , HOH C:74
BINDING SITE FOR RESIDUE CA C 36
12
BC3
SOFTWARE
ALA C:1 , ASN C:2 , CGU C:6 , CGU C:7 , CGU C:16 , CGU C:26
BINDING SITE FOR RESIDUE CA C 37
13
BC4
SOFTWARE
ALA C:1 , CGU C:6 , CGU C:16 , CGU C:20 , HOH C:59
BINDING SITE FOR RESIDUE CA C 38
14
BC5
SOFTWARE
CGU C:20 , HOH C:63 , HOH C:66 , HOH C:79 , HOH C:80
BINDING SITE FOR RESIDUE CA C 39
15
BC6
SOFTWARE
CGU C:14 , CGU C:19 , HOH C:67 , HOH C:99
BINDING SITE FOR RESIDUE MG C 40
16
BC7
SOFTWARE
GLU B:86 , HOH B:658 , CGU D:25 , CGU D:29
BINDING SITE FOR RESIDUE MG D 34
17
BC8
SOFTWARE
GLU B:86 , CGU D:7 , CGU D:26 , CGU D:29 , HOH D:54
BINDING SITE FOR RESIDUE CA D 35
18
BC9
SOFTWARE
CGU D:7 , CGU D:16 , CGU D:26 , CGU D:29 , HOH D:56 , HOH D:57 , HOH D:60
BINDING SITE FOR RESIDUE CA D 36
19
CC1
SOFTWARE
ALA D:1 , ASN D:2 , CGU D:6 , CGU D:7 , CGU D:16 , CGU D:26
BINDING SITE FOR RESIDUE CA D 37
20
CC2
SOFTWARE
ALA D:1 , CGU D:6 , CGU D:16 , CGU D:20 , HOH D:77
BINDING SITE FOR RESIDUE CA D 38
21
CC3
SOFTWARE
CGU D:20 , HOH D:58 , HOH D:69 , HOH D:70 , HOH D:75
BINDING SITE FOR RESIDUE CA D 39
22
CC4
SOFTWARE
CGU D:14 , CGU D:19 , HOH D:68 , HOH D:87
BINDING SITE FOR RESIDUE MG D 40
[
close Site info
]
SAPs(SNPs)/Variants
(7, 14)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_006639 (A1T, chain C/D, )
2: VAR_006640 (E7D, chain C/D, )
3: VAR_006641 (R9C, chain C/D, )
4: VAR_006643 (R15G, chain C/D, )
5: VAR_006644 (R15Q, chain C/D, )
6: VAR_006642 (R15W, chain C/D, )
7: VAR_006645 (E20A, chain C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_006639
A
43
T
PROC_HUMAN
Polymorphism
---
C/D
A
1
T
2
UniProt
VAR_006640
E
49
D
PROC_HUMAN
Unclassified
---
C/D
E
7
D
3
UniProt
VAR_006641
R
51
C
PROC_HUMAN
Unclassified
---
C/D
R
9
C
4
UniProt
VAR_006643
R
57
G
PROC_HUMAN
Unclassified
---
C/D
R
15
G
5
UniProt
VAR_006644
R
57
Q
PROC_HUMAN
Unclassified
---
C/D
R
15
Q
6
UniProt
VAR_006642
R
57
W
PROC_HUMAN
Disease (THPH3)
---
C/D
R
15
W
7
UniProt
VAR_006645
E
62
A
PROC_HUMAN
Disease (THPH3)
---
C/D
E
20
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GLA_1 (C:16-33,D:16-33)
;
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.
PROC_HUMAN
58-83
2
C:16-33
D:16-33
[
close PROSITE info
]
Exons
(4, 7)
Info
All Exons
Exon 1.3a (A:7-7 | -)
Exon 1.4 (A:7-91 | B:8-91)
Exon 1.5 (A:91-178 | B:91-180)
Exon 2.3a (C:1-33 | D:1-33)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6a
5: Boundary 2.2e/2.3a
6: Boundary 2.3a/2.4a
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
1.3a
ENST00000216968
3a
ENSE00001463636
chr20:
33759774-33760027
254
EPCR_HUMAN
1-24
24
1
A:7-7
-
1
-
1.4
ENST00000216968
4
ENSE00000661565
chr20:
33762505-33762756
252
EPCR_HUMAN
24-108
85
2
A:7-91
B:8-91
85
84
1.5
ENST00000216968
5
ENSE00000661566
chr20:
33763971-33764249
279
EPCR_HUMAN
108-201
94
2
A:91-178
B:91-180
88
90
1.6a
ENST00000216968
6a
ENSE00001463602
chr20:
33764501-33765164
664
EPCR_HUMAN
201-238
38
0
-
-
2.1a
ENST00000234071
1a
ENSE00001747079
chr2:
128176003-128176068
66
PROC_HUMAN
-
0
0
-
-
2.2e
ENST00000234071
2e
ENSE00000857263
chr2:
128177498-128177588
91
PROC_HUMAN
1-24
24
0
-
-
2.3a
ENST00000234071
3a
ENSE00001019166
chr2:
128178859-128179025
167
PROC_HUMAN
24-79
56
2
C:1-33
D:1-33
33
33
2.4a
ENST00000234071
4a
ENSE00001657237
chr2:
128180493-128180517
25
PROC_HUMAN
80-88
9
0
-
-
2.4h
ENST00000234071
4h
ENSE00000775732
chr2:
128180610-128180747
138
PROC_HUMAN
88-134
47
0
-
-
2.4k
ENST00000234071
4k
ENSE00001019181
chr2:
128180850-128180984
135
PROC_HUMAN
134-179
46
0
-
-
2.5b
ENST00000234071
5b
ENSE00000775730
chr2:
128183661-128183803
143
PROC_HUMAN
179-226
48
0
-
-
2.6
ENST00000234071
6
ENSE00000775729
chr2:
128184681-128184798
118
PROC_HUMAN
227-266
40
0
-
-
2.7d
ENST00000234071
7d
ENSE00001853552
chr2:
128185933-128186822
890
PROC_HUMAN
266-461
196
0
-
-
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3jtca_ (A:)
1b: SCOP_d3jtcb_ (B:)
2a: SCOP_d3jtcc_ (C:)
2b: SCOP_d3jtcd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(24)
1a
d3jtca_
A:
1b
d3jtcb_
B:
Class
:
Small proteins
(3458)
Fold
:
GLA-domain
(44)
Superfamily
:
GLA-domain
(44)
Family
:
GLA-domain
(37)
Protein domain
:
Coagulation factor XIV (Protein C)
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d3jtcc_
C:
2b
d3jtcd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_MHC_I_3jtcB01 (B:53-180)
1b: PFAM_MHC_I_3jtcB02 (B:53-180)
2a: PFAM_Gla_3jtcD01 (D:5-33)
2b: PFAM_Gla_3jtcD02 (D:5-33)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Homo sapiens (Human)
(144)
1a
MHC_I-3jtcB01
B:53-180
1b
MHC_I-3jtcB02
B:53-180
Clan
:
no clan defined [family: Gla]
(24)
Family
:
Gla
(24)
Homo sapiens (Human)
(14)
2a
Gla-3jtcD01
D:5-33
2b
Gla-3jtcD02
D:5-33
[
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 B
Chain C
Chain D
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 (95 KB)
Header - Asym.Unit
Biol.Unit 1 (45 KB)
Header - Biol.Unit 1
Biol.Unit 2 (44 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
3JTC
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help