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1Y0V
Biol. Unit 6
Info
Asym.Unit (887 KB)
Biol.Unit 1 (154 KB)
Biol.Unit 2 (153 KB)
Biol.Unit 3 (153 KB)
Biol.Unit 4 (153 KB)
Biol.Unit 5 (153 KB)
Biol.Unit 6 (154 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ANTHRAX EDEMA FACTOR (EF) IN COMPLEX WITH CALMODULIN AND PYROPHOSPHATE
Authors
:
Y. Shen, N. L. Zhukovskaya, Q. Guo, J. Florian, W. -J. Tang
Date
:
16 Nov 04 (Deposition) - 03 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.60
Chains
:
Asym. Unit : A,B,C,D,E,F,H,I,J,K,L,M
Biol. Unit 1: A,H (1x)
Biol. Unit 2: B,I (1x)
Biol. Unit 3: C,J (1x)
Biol. Unit 4: D,K (1x)
Biol. Unit 5: E,L (1x)
Biol. Unit 6: F,M (1x)
Keywords
:
Calcium-Independent, Calmodulin, Anthrax Edema Factor, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Shen, N. L. Zhukovskaya, Q. Guo, W. -J. Tang
Calcium-Independent Calmodulin Binding And Two-Metal-Ion Catalytic Mechanism Of Anthrax Edema Factor
Embo J. V. 24 929 2005
(for further references see the
PDB file header
)
[
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]
Hetero Components
(1, 1)
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)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
1q: CALCIUM ION (CAq)
1r: CALCIUM ION (CAr)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
3a: PYROPHOSPHATE 2- (POPa)
3b: PYROPHOSPHATE 2- (POPb)
3c: PYROPHOSPHATE 2- (POPc)
3d: PYROPHOSPHATE 2- (POPd)
3e: PYROPHOSPHATE 2- (POPe)
3f: PYROPHOSPHATE 2- (POPf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
[
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]
Sites
(5, 5)
Info
All Sites
1: AC6 (SOFTWARE)
2: CC4 (SOFTWARE)
3: CC5 (SOFTWARE)
4: CC6 (SOFTWARE)
5: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC6
SOFTWARE
ASP F:491 , ASP F:493 , HIS F:577
BINDING SITE FOR RESIDUE MG F 905
2
CC4
SOFTWARE
ASP M:20 , ASP M:22 , ASP M:24 , THR M:26
BINDING SITE FOR RESIDUE CA M 711
3
CC5
SOFTWARE
ASP M:129 , ASP M:131 , ASP M:133 , GLN M:135 , GLU M:140
BINDING SITE FOR RESIDUE CA M 811
4
CC6
SOFTWARE
ASP M:93 , ASP M:95 , ASN M:97 , TYR M:99 , GLU M:104
BINDING SITE FOR RESIDUE CA M 812
5
DC3
SOFTWARE
LYS F:346 , SER F:354 , LYS F:372
BINDING SITE FOR RESIDUE POP F 906
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (M:116-148)
2: EF_HAND_1 (M:129-141)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
CAM2B_XENLA
8-43
44-79
81-116
117-149
4
-
-
-
-
-
M:7-42
-
-
-
-
-
M:43-78
-
-
-
-
-
M:80-115
-
-
-
-
-
M:116-148
CAM2A_XENLA
8-43
44-79
81-116
117-149
4
-
-
-
-
-
M:7-42
-
-
-
-
-
M:43-78
-
-
-
-
-
M:80-115
-
-
-
-
-
M:116-148
CALM1_XENLA
8-43
44-79
81-116
117-149
4
-
-
-
-
-
M:7-42
-
-
-
-
-
M:43-78
-
-
-
-
-
M:80-115
-
-
-
-
-
M:116-148
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CAM2B_XENLA
21-33
57-69
94-106
130-142
4
-
-
-
-
-
M:20-32
-
-
-
-
-
M:56-68
-
-
-
-
-
M:93-105
-
-
-
-
-
M:129-141
CAM2A_XENLA
21-33
57-69
94-106
130-142
4
-
-
-
-
-
M:20-32
-
-
-
-
-
M:56-68
-
-
-
-
-
M:93-105
-
-
-
-
-
M:129-141
CALM1_XENLA
21-33
57-69
94-106
130-142
4
-
-
-
-
-
M:20-32
-
-
-
-
-
M:56-68
-
-
-
-
-
M:93-105
-
-
-
-
-
M:129-141
[
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1y0vh1 (H:5-148)
1b: SCOP_d1y0vi1 (I:5-148)
1c: SCOP_d1y0vj1 (J:5-148)
1d: SCOP_d1y0vk1 (K:5-148)
1e: SCOP_d1y0vl1 (L:5-148)
1f: SCOP_d1y0vm1 (M:5-148)
View:
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(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
Calmodulin-like
(356)
Protein domain
:
Calmodulin
(152)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(13)
1a
d1y0vh1
H:5-148
1b
d1y0vi1
I:5-148
1c
d1y0vj1
J:5-148
1d
d1y0vk1
K:5-148
1e
d1y0vl1
L:5-148
1f
d1y0vm1
M:5-148
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_1y0vA01 (A:64-291)
1b: CATH_1y0vB01 (B:64-291)
1c: CATH_1y0vC01 (C:64-291)
1d: CATH_1y0vD01 (D:64-291)
1e: CATH_1y0vE01 (E:64-291)
1f: CATH_1y0vF01 (F:64-291)
2a: CATH_1y0vH01 (H:3-78)
2b: CATH_1y0vK01 (K:3-78)
2c: CATH_1y0vL01 (L:3-78)
2d: CATH_1y0vM01 (M:3-78)
2e: CATH_1y0vH02 (H:79-146)
2f: CATH_1y0vI02 (I:79-146)
2g: CATH_1y0vJ02 (J:79-146)
2h: CATH_1y0vK02 (K:79-146)
2i: CATH_1y0vL02 (L:79-146)
2j: CATH_1y0vM02 (M:79-146)
2k: CATH_1y0vI01 (I:3-78)
2l: CATH_1y0vJ01 (J:3-78)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Collagenase (Catalytic Domain)
(236)
Homologous Superfamily
:
Collagenase (Catalytic Domain)
(234)
Bacillus anthracis. Organism_taxid: 1392.
(15)
1a
1y0vA01
A:64-291
1b
1y0vB01
B:64-291
1c
1y0vC01
C:64-291
1d
1y0vD01
D:64-291
1e
1y0vE01
E:64-291
1f
1y0vF01
F:64-291
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Bacillus anthracis. Organism_taxid: 1392.
(10)
2a
1y0vH01
H:3-78
2b
1y0vK01
K:3-78
2c
1y0vL01
L:3-78
2d
1y0vM01
M:3-78
2e
1y0vH02
H:79-146
2f
1y0vI02
I:79-146
2g
1y0vJ02
J:79-146
2h
1y0vK02
K:79-146
2i
1y0vL02
L:79-146
2j
1y0vM02
M:79-146
2k
1y0vI01
I:3-78
2l
1y0vJ01
J:3-78
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_ATLF_1y0vF01 (F:64-277)
1b: PFAM_ATLF_1y0vF02 (F:64-277)
1c: PFAM_ATLF_1y0vF03 (F:64-277)
1d: PFAM_ATLF_1y0vF04 (F:64-277)
1e: PFAM_ATLF_1y0vF05 (F:64-277)
1f: PFAM_ATLF_1y0vF06 (F:64-277)
2a: PFAM_Anthrax_toxA_1y0vF07 (F:293-472)
2b: PFAM_Anthrax_toxA_1y0vF08 (F:293-472)
2c: PFAM_Anthrax_toxA_1y0vF09 (F:293-472)
2d: PFAM_Anthrax_toxA_1y0vF10 (F:293-472)
2e: PFAM_Anthrax_toxA_1y0vF11 (F:293-472)
2f: PFAM_Anthrax_toxA_1y0vF12 (F:293-472)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: ATLF]
(15)
Family
:
ATLF
(15)
Bacillus anthracis
(15)
1a
ATLF-1y0vF01
F:64-277
1b
ATLF-1y0vF02
F:64-277
1c
ATLF-1y0vF03
F:64-277
1d
ATLF-1y0vF04
F:64-277
1e
ATLF-1y0vF05
F:64-277
1f
ATLF-1y0vF06
F:64-277
Clan
:
no clan defined [family: Anthrax_toxA]
(16)
Family
:
Anthrax_toxA
(16)
Bacillus anthracis
(13)
2a
Anthrax_toxA-1y0vF07
F:293-472
2b
Anthrax_toxA-1y0vF08
F:293-472
2c
Anthrax_toxA-1y0vF09
F:293-472
2d
Anthrax_toxA-1y0vF10
F:293-472
2e
Anthrax_toxA-1y0vF11
F:293-472
2f
Anthrax_toxA-1y0vF12
F:293-472
[
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]
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