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1J34
Asym. Unit
Info
Asym.Unit (69 KB)
Biol.Unit 1 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MG(II)-AND CA(II)-BOUND GLA DOMAIN OF FACTOR IX COMPLEXED WITH BINDING PROTEIN
Authors
:
Y. Shikamoto, T. Morita, Z. Fujimoto, H. Mizuno
Date
:
20 Jan 03 (Deposition) - 08 Jul 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Magnesium Ion, Calcium Ion, Gla Domain, Protein Binding/Blood Clotting Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Shikamoto, T. Morita, Z. Fujimoto, H. Mizuno
Crystal Structure Of Mg2+- And Ca2+-Bound Gla Domain Of Factor Ix Complexed With Binding Protein
J. Biol. Chem. V. 278 24090 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 22)
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)
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)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
7
Ligand/Ion
CALCIUM ION
2
CGU
12
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
3
MG
3
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:98 , CGU C:426 , CGU C:430 , HOH C:1006
BINDING SITE FOR RESIDUE MG C 501
02
AC2
SOFTWARE
HOH B:804 , CGU C:408 , CGU C:427 , CGU C:430 , HOH C:807
BINDING SITE FOR RESIDUE CA C 502
03
AC3
SOFTWARE
CGU C:408 , CGU C:417 , CGU C:427 , CGU C:430 , HOH C:803 , HOH C:805 , HOH C:810
BINDING SITE FOR RESIDUE CA C 503
04
AC4
SOFTWARE
TYR C:401 , ASN C:402 , CGU C:407 , CGU C:408 , CGU C:417 , CGU C:427
BINDING SITE FOR RESIDUE CA C 504
05
AC5
SOFTWARE
TYR C:401 , CGU C:407 , CGU C:417 , CGU C:421 , HOH C:808 , HOH C:816
BINDING SITE FOR RESIDUE CA C 505
06
AC6
SOFTWARE
CGU C:421 , HOH C:646 , HOH C:813 , HOH C:817 , HOH C:847 , HOH C:1011
BINDING SITE FOR RESIDUE CA C 506
07
AC7
SOFTWARE
CGU C:415 , CGU C:420 , HOH C:821 , HOH C:826
BINDING SITE FOR RESIDUE MG C 507
08
AC8
SOFTWARE
CGU C:436 , CGU C:440 , HOH C:802 , HOH C:806
BINDING SITE FOR RESIDUE MG C 508
09
AC9
SOFTWARE
SER A:41 , GLU A:43 , GLU A:47 , GLU A:128 , HOH A:809 , HOH A:837
BINDING SITE FOR RESIDUE CA A 511
10
BC1
SOFTWARE
SER B:241 , GLN B:243 , GLU B:247 , GLU B:320 , HOH B:818 , HOH B:820
BINDING SITE FOR RESIDUE CA B 512
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(4, 6)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_2 (A:9-128,A:9-128,B:209-320)
2: GLA_2 (C:401-446)
3: GLA_1 (C:417-442)
4: C_TYPE_LECTIN_1 (A:102-127,B:296-319,A:102-127)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
C_TYPE_LECTIN_2
PS50041
C-type lectin domain profile.
SLA_PROFL
9-128
1
A:9-128
SL9A_PROFL
32-151
1
A:9-128
SL9B_PROFL
32-143
1
B:209-320
2
GLA_2
PS50998
Gla domain profile.
FA9_BOVIN
47-93
1
C:401-446
3
GLA_1
PS00011
Vitamin K-dependent carboxylation domain.
FA9_BOVIN
63-88
1
C:417-442
4
C_TYPE_LECTIN_1
PS00615
C-type lectin domain signature.
SLA_PROFL
102-127
1
A:102-127
SL9B_PROFL
119-142
1
B:296-319
SL9A_PROFL
125-150
1
A:102-127
[
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Exons
(2, 2)
Info
All Exons
Exon 1.2 (C:401-438)
Exon 1.3 (C:439-446)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
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
ENSBTAT00000005227
1
ENSBTAE00000424634
X:12957216-12957316
101
FA9_BOVIN
1-30
30
0
-
-
1.2
ENSBTAT00000005227
2
ENSBTAE00000425150
X:12975755-12975918
164
FA9_BOVIN
30-84
55
1
C:401-438
38
1.3
ENSBTAT00000005227
3
ENSBTAE00000410831
X:12976116-12976140
25
FA9_BOVIN
85-93
9
1
C:439-446
8
1.4
ENSBTAT00000005227
4
ENSBTAE00000387324
X:12980325-12980438
114
FA9_BOVIN
93-131
39
0
-
-
1.5
ENSBTAT00000005227
5
ENSBTAE00000388223
X:12987557-12987685
129
FA9_BOVIN
131-174
44
0
-
-
1.6b
ENSBTAT00000005227
6b
ENSBTAE00000041994
X:12990058-12990263
206
FA9_BOVIN
174-242
69
0
-
-
1.7
ENSBTAT00000005227
7
ENSBTAE00000041996
X:12999018-12999132
115
FA9_BOVIN
243-281
39
0
-
-
1.8
ENSBTAT00000005227
8
ENSBTAE00000041998
X:13001262-13003332
2071
FA9_BOVIN
281-462
182
0
-
-
[
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]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1j34a_ (A:)
2a: SCOP_d1j34b_ (B:)
3a: SCOP_d1j34c_ (C:)
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)
(
)
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(
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
C-type lectin-like
(322)
Superfamily
:
C-type lectin-like
(322)
Family
:
C-type lectin domain
(182)
Protein domain
:
Snake coagglutinin alpha chain
(23)
Habu snake (Trimeresurus flavoviridis) [TaxId: 88087]
(6)
1a
d1j34a_
A:
Protein domain
:
Snake coagglutinin beta chain
(23)
Habu snake (Trimeresurus flavoviridis) [TaxId: 88087]
(6)
2a
d1j34b_
B:
Class
:
Small proteins
(3458)
Fold
:
GLA-domain
(44)
Superfamily
:
GLA-domain
(44)
Family
:
GLA-domain
(37)
Protein domain
:
Coagulation factor IX (IXa)
(7)
Cow (Bos taurus) [TaxId:9913]
(2)
3a
d1j34c_
C:
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1j34A00 (A:1-129)
1b: CATH_1j34B00 (B:201-323)
2a: CATH_1j34C00 (C:401-446)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Mannose-Binding Protein A; Chain A
(180)
Homologous Superfamily
:
Mannose-Binding Protein A, subunit A
(180)
Trimeresurus flavoviridis. Organism_taxid: 88087.
(7)
1a
1j34A00
A:1-129
1b
1j34B00
B:201-323
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Coagulation Factor IX
(11)
Homologous Superfamily
:
Coagulation Factor IX
(11)
Trimeresurus flavoviridis. Organism_taxid: 88087.
(2)
2a
1j34C00
C:401-446
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Chain C
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