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1IOD
Biol. Unit 3
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Asym.Unit (64 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (109 KB)
Biol.Unit 3 (110 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X
Authors
:
H. Mizuno, Z. Fujimoto, H. Atoda, T. Morita
Date
:
27 Feb 01 (Deposition) - 27 Jun 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,G
Biol. Unit 1: A,B,G (1x)
Biol. Unit 2: A,B,G (2x)
Biol. Unit 3: A,B,G (2x)
Keywords
:
Calcium Bridging, Domain Swapping, Hydrolase/Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Mizuno, Z. Fujimoto, H. Atoda, T. Morita
Crystal Structure Of An Anticoagulant Protein In Complex With The Gla Domain Of Factor X.
Proc. Natl. Acad. Sci. Usa V. 98 7230 2001
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 24)
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)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
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
CA
-1
Ligand/Ion
CALCIUM ION
2
CGU
24
Mod. Amino Acid
GAMMA-CARBOXY-GLUTAMIC ACID
[
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]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:41 , GLU A:43 , GLU A:47 , GLU A:128 , HOH A:568
BINDING SITE FOR RESIDUE CA A 501
02
AC2
SOFTWARE
SER B:241 , GLN B:243 , GLU B:247 , GLU B:320 , HOH B:529 , HOH B:554
BINDING SITE FOR RESIDUE CA B 502
03
AC3
SOFTWARE
GLU A:98 , HOH B:505 , CGU G:425 , CGU G:429
BINDING SITE FOR RESIDUE CA G 503
04
AC4
SOFTWARE
HOH G:47 , HOH G:62 , CGU G:407 , CGU G:426 , CGU G:429
BINDING SITE FOR RESIDUE CA G 504
05
AC5
SOFTWARE
HOH G:63 , HOH G:102 , HOH G:125 , CGU G:407 , CGU G:416 , CGU G:426 , CGU G:429 , CA G:506
BINDING SITE FOR RESIDUE CA G 505
06
AC6
SOFTWARE
ALA G:401 , ASN G:402 , CGU G:406 , CGU G:407 , CGU G:416 , CGU G:426 , CA G:505
BINDING SITE FOR RESIDUE CA G 506
07
AC7
SOFTWARE
HOH G:123 , ALA G:401 , CGU G:406 , CGU G:416 , CGU G:420
BINDING SITE FOR RESIDUE CA G 507
08
AC8
SOFTWARE
HOH G:37 , HOH G:143 , HOH G:149 , HOH G:190 , CGU G:420
BINDING SITE FOR RESIDUE CA G 508
09
AC9
SOFTWARE
HOH G:204 , HOH G:218 , CGU G:414 , CGU G:419
BINDING SITE FOR RESIDUE CA G 509
10
BC1
SOFTWARE
CGU G:435 , CGU G:439
BINDING SITE FOR RESIDUE CA G 510
11
BC2
SOFTWARE
SER A:80 , GLU A:82 , HOH A:580
BINDING SITE FOR RESIDUE CA A 511
12
BC3
SOFTWARE
ASP A:1 , HOH A:575
BINDING SITE FOR RESIDUE CA A 512
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 10)
Info
All PROSITE Patterns/Profiles
1: C_TYPE_LECTIN_2 (A:9-128)
2: GLA_1 (G:416-441)
3: C_TYPE_LECTIN_1 (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.
SLAB_DEIAC
32-143
2
B:209-320
SLUA_DEIAC
32-151
2
A:9-128
2
GLA_1
PS00011
Vitamin K-dependent carboxylation domain.
FA10_BOVIN
56-81
2
G:416-441
3
C_TYPE_LECTIN_1
PS00615
C-type lectin domain signature.
SLAB_DEIAC
119-142
2
B:296-319
SLUA_DEIAC
125-150
2
A:102-127
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1ioda_ (A:)
2a: SCOP_d1iodb_ (B:)
3a: SCOP_d1iodg_ (G:)
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Classes
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)
(
)
Folds
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(
)
Superfamilies
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)
(
)
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(
)
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)
Hundred-pace snake (Deinagkistrodon acutus), different isoforms [TaxId: 36307]
(3)
1a
d1ioda_
A:
Protein domain
:
Snake coagglutinin beta chain
(23)
Sharp-nosed viper (Deinagkistrodon acutus) [TaxId: 36307]
(3)
2a
d1iodb_
B:
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)
3a
d1iodg_
G:
[
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]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1iodA00 (A:1-129)
1b: CATH_1iodB00 (B:201-323)
2a: CATH_1iodG00 (G:401-444)
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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)
Chinese moccasin (Deinagkistrodon acutus)
(3)
1a
1iodA00
A:1-129
1b
1iodB00
B:201-323
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Coagulation Factor IX
(11)
Homologous Superfamily
:
Coagulation Factor IX
(11)
Chinese moccasin (Deinagkistrodon acutus)
(1)
2a
1iodG00
G:401-444
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain G
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (64 KB)
Header - Asym.Unit
Biol.Unit 1 (56 KB)
Header - Biol.Unit 1
Biol.Unit 2 (109 KB)
Header - Biol.Unit 2
Biol.Unit 3 (110 KB)
Header - Biol.Unit 3
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