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Biol. Unit 2
Info
Asym.Unit (95 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
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(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
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Hetero Components
(3, 13)
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
-1
Ligand/Ion
CALCIUM ION
2
CGU
9
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
NDG
-1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6
PTY
1
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC7 (SOFTWARE)
06: BC8 (SOFTWARE)
07: BC9 (SOFTWARE)
08: CC1 (SOFTWARE)
09: CC2 (SOFTWARE)
10: CC3 (SOFTWARE)
11: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
AC6
SOFTWARE
ALA B:90 , PRO B:92 , ASN B:119 , HOH B:626 , HOH B:701
BINDING SITE FOR RESIDUE NAG B 601
03
AC7
SOFTWARE
ASN B:155 , HOH B:660 , HOH B:686
BINDING SITE FOR RESIDUE NAG B 602
04
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
05
BC7
SOFTWARE
GLU B:86 , HOH B:658 , CGU D:25 , CGU D:29
BINDING SITE FOR RESIDUE MG D 34
06
BC8
SOFTWARE
GLU B:86 , CGU D:7 , CGU D:26 , CGU D:29 , HOH D:54
BINDING SITE FOR RESIDUE CA D 35
07
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
08
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
09
CC2
SOFTWARE
ALA D:1 , CGU D:6 , CGU D:16 , CGU D:20 , HOH D:77
BINDING SITE FOR RESIDUE CA D 38
10
CC3
SOFTWARE
CGU D:20 , HOH D:58 , HOH D:69 , HOH D:70 , HOH D:75
BINDING SITE FOR RESIDUE CA D 39
11
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, 7)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_006639 (A1T, chain D, )
2: VAR_006640 (E7D, chain D, )
3: VAR_006641 (R9C, chain D, )
4: VAR_006643 (R15G, chain D, )
5: VAR_006644 (R15Q, chain D, )
6: VAR_006642 (R15W, chain D, )
7: VAR_006645 (E20A, chain 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
---
D
A
1
T
2
UniProt
VAR_006640
E
49
D
PROC_HUMAN
Unclassified
---
D
E
7
D
3
UniProt
VAR_006641
R
51
C
PROC_HUMAN
Unclassified
---
D
R
9
C
4
UniProt
VAR_006643
R
57
G
PROC_HUMAN
Unclassified
---
D
R
15
G
5
UniProt
VAR_006644
R
57
Q
PROC_HUMAN
Unclassified
---
D
R
15
Q
6
UniProt
VAR_006642
R
57
W
PROC_HUMAN
Disease (THPH3)
---
D
R
15
W
7
UniProt
VAR_006645
E
62
A
PROC_HUMAN
Disease (THPH3)
---
D
E
20
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: GLA_1 (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
1
-
D:16-33
[
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]
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, 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:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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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
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Chain D
Asymmetric Unit 1
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