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Asym. Unit
Info
Asym.Unit (321 KB)
Biol.Unit 1 (311 KB)
Biol.Unit 2 (111 KB)
Biol.Unit 3 (108 KB)
Biol.Unit 4 (105 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE EF3-CAM COMPLEXED WITH PMEAPP
Authors
:
Y. Shen, W. J. Tang
Date
:
04 Jun 03 (Deposition) - 10 Feb 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: C,F (1x)
Biol. Unit 3: A,D (1x)
Biol. Unit 4: B,E (1x)
Keywords
:
Edema Factor, Cam, Prodrug Complex, Lyase-Metal Binding Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Shen, N. L. Zhukovskaya, M. I. Zimmer, S. Soelaiman, P. Bergson, C. R. Wang, C. S. Gibbs, W. J. Tang
Selective Inhibition Of Anthrax Edema Factor By Adefovir, A Drug For Chronic Hepatitis B Virus Infection.
Proc. Natl. Acad. Sci. Usa V. 101 3242 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
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)
2a: (ADENIN-9-YL-ETHOXYMETHYL)-HYDROXY... (EMAa)
2b: (ADENIN-9-YL-ETHOXYMETHYL)-HYDROXY... (EMAb)
2c: (ADENIN-9-YL-ETHOXYMETHYL)-HYDROXY... (EMAc)
3a: YTTERBIUM (III) ION (YBa)
3b: YTTERBIUM (III) ION (YBb)
3c: YTTERBIUM (III) ION (YBc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
EMA
3
Ligand/Ion
(ADENIN-9-YL-ETHOXYMETHYL)-HYDROXYPHOSPHINYL-DIPHOSPHATE
3
YB
3
Ligand/Ion
YTTERBIUM (III) ION
[
close Hetero Component info
]
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
ASP D:129 , ASP D:131 , ASP D:133 , GLN D:135 , GLU D:140
BINDING SITE FOR RESIDUE CA D 800
02
AC2
SOFTWARE
ASP D:93 , ASP D:95 , ASN D:97 , TYR D:99 , GLU D:104
BINDING SITE FOR RESIDUE CA D 801
03
AC3
SOFTWARE
ASP E:131 , ASP E:133 , GLN E:135 , GLU E:140
BINDING SITE FOR RESIDUE CA E 802
04
AC4
SOFTWARE
ASP E:93 , ASP E:95 , ASN E:97 , TYR E:99 , GLU E:104
BINDING SITE FOR RESIDUE CA E 803
05
AC5
SOFTWARE
ASP F:129 , ASP F:131 , ASP F:133 , GLN F:135 , GLU F:140
BINDING SITE FOR RESIDUE CA F 804
06
AC6
SOFTWARE
ASP F:93 , ASP F:95 , ASN F:97 , TYR F:99 , GLU F:104
BINDING SITE FOR RESIDUE CA F 805
07
AC7
SOFTWARE
ASP A:491 , ASP A:493 , HIS A:577 , EMA A:1999
BINDING SITE FOR RESIDUE YB A 901
08
AC8
SOFTWARE
ASP B:491 , ASP B:493 , HIS B:577 , EMA B:2999
BINDING SITE FOR RESIDUE YB B 902
09
AC9
SOFTWARE
ASP C:491 , ASP C:493 , HIS C:577 , EMA C:3999
BINDING SITE FOR RESIDUE YB C 903
10
BC1
SOFTWARE
HOH A:7 , ARG A:329 , LYS A:346 , LEU A:348 , LYS A:353 , SER A:354 , LYS A:372 , ALA A:490 , ASP A:493 , GLY A:547 , THR A:548 , HIS A:577 , GLY A:578 , THR A:579 , ASN A:583 , YB A:901
BINDING SITE FOR RESIDUE EMA A 1999
11
BC2
SOFTWARE
HOH B:12 , ARG B:329 , LYS B:346 , LYS B:353 , SER B:354 , LYS B:372 , ALA B:490 , ASP B:493 , GLY B:547 , THR B:548 , HIS B:577 , GLY B:578 , ASN B:583 , YB B:902
BINDING SITE FOR RESIDUE EMA B 2999
12
BC3
SOFTWARE
HOH C:14 , ARG C:329 , LYS C:346 , LYS C:353 , SER C:354 , LYS C:372 , ASP C:493 , THR C:548 , HIS C:577 , GLY C:578 , THR C:579 , ASN C:583 , YB C:903
BINDING SITE FOR RESIDUE EMA C 3999
[
close Site info
]
SAPs(SNPs)/Variants
(11, 33)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_069222 (N53I, chain D/E/F, )
02: VAR_048585 (M72T, chain D/E/F, )
03: VAR_073275 (F89L, chain D/E/F, )
04: VAR_073276 (D95V, chain D/E/F, )
05: VAR_073277 (N97I, chain D/E/F, )
06: VAR_069223 (N97S, chain D/E/F, )
07: VAR_073278 (D129G, chain D/E/F, )
08: VAR_073279 (D131E, chain D/E/F, )
09: VAR_073280 (D133H, chain D/E/F, )
10: VAR_073281 (Q135P, chain D/E/F, )
11: VAR_073282 (F141L, chain D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_069222
N
54
I
CALM_HUMAN
Disease (CPVT4)
---
D/E/F
N
53
I
02
UniProt
VAR_048585
M
73
T
CALM_HUMAN
Polymorphism
41389749
D/E/F
M
72
T
03
UniProt
VAR_073275
F
90
L
CALM_HUMAN
Disease (LQT14)
---
D/E/F
F
89
L
04
UniProt
VAR_073276
D
96
V
CALM_HUMAN
Disease (LQT15)
---
D/E/F
D
95
V
05
UniProt
VAR_073277
N
98
I
CALM_HUMAN
Disease (LQT15)
---
D/E/F
N
97
I
06
UniProt
VAR_069223
N
98
S
CALM_HUMAN
Disease (CPVT4)
---
D/E/F
N
97
S
07
UniProt
VAR_073278
D
130
G
CALM_HUMAN
Disease (LQT14)
---
D/E/F
D
129
G
08
UniProt
VAR_073279
D
132
E
CALM_HUMAN
Disease (LQT15)
---
D/E/F
D
131
E
09
UniProt
VAR_073280
D
134
H
CALM_HUMAN
Disease (LQT15)
---
D/E/F
D
133
H
10
UniProt
VAR_073281
Q
136
P
CALM_HUMAN
Disease (LQT15)
---
D/E/F
Q
135
P
11
UniProt
VAR_073282
F
142
L
CALM_HUMAN
Disease (LQT14)
---
D/E/F
F
141
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 24)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (D:7-42,E:7-42,F:7-42|D:43-78,E:43-...)
2: EF_HAND_1 (D:20-32,E:20-32,F:20-32|D:56-68,E:...)
;
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.
CALM1_HUMAN
8-43
44-79
81-116
117-149
12
D:7-42
E:7-42
F:7-42
D:43-78
E:43-78
F:43-78
D:80-115
E:80-115
F:80-115
D:116-147
E:116-147
F:116-147
CALM2_HUMAN
8-43
44-79
81-116
117-149
12
D:7-42
E:7-42
F:7-42
D:43-78
E:43-78
F:43-78
D:80-115
E:80-115
F:80-115
D:116-147
E:116-147
F:116-147
CALM3_HUMAN
8-43
44-79
81-116
117-149
12
D:7-42
E:7-42
F:7-42
D:43-78
E:43-78
F:43-78
D:80-115
E:80-115
F:80-115
D:116-147
E:116-147
F:116-147
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CALM1_HUMAN
21-33
57-69
94-106
130-142
12
D:20-32
E:20-32
F:20-32
D:56-68
E:56-68
F:56-68
D:93-105
E:93-105
F:93-105
D:129-141
E:129-141
F:129-141
CALM2_HUMAN
21-33
57-69
94-106
130-142
12
D:20-32
E:20-32
F:20-32
D:56-68
E:56-68
F:56-68
D:93-105
E:93-105
F:93-105
D:129-141
E:129-141
F:129-141
CALM3_HUMAN
21-33
57-69
94-106
130-142
12
D:20-32
E:20-32
F:20-32
D:56-68
E:56-68
F:56-68
D:93-105
E:93-105
F:93-105
D:129-141
E:129-141
F:129-141
[
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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.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1pk0d_ (D:)
1b: SCOP_d1pk0e_ (E:)
1c: SCOP_d1pk0f_ (F:)
2a: SCOP_d1pk0a_ (A:)
2b: SCOP_d1pk0b_ (B:)
2c: SCOP_d1pk0c_ (C:)
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Human (Homo sapiens) [TaxId: 9606]
(74)
1a
d1pk0d_
D:
1b
d1pk0e_
E:
1c
d1pk0f_
F:
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Adenylylcyclase toxin (the edema factor)
(7)
Superfamily
:
Adenylylcyclase toxin (the edema factor)
(7)
Family
:
Adenylylcyclase toxin (the edema factor)
(7)
Protein domain
:
Adenylylcyclase toxin (the edema factor)
(7)
Anthrax bacillus (Bacillus anthracis) [TaxId: 1392]
(7)
2a
d1pk0a_
A:
2b
d1pk0b_
B:
2c
d1pk0c_
C:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1pk0D01 (D:5-78)
1b: CATH_1pk0D02 (D:79-146)
1c: CATH_1pk0E02 (E:79-146)
1d: CATH_1pk0F02 (F:79-146)
1e: CATH_1pk0E01 (E:5-78)
1f: CATH_1pk0F01 (F:5-78)
View:
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(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Recoverin; domain 1
(474)
Homologous Superfamily
:
EF-hand
(412)
Bacillus anthracis. Organism_taxid: 1392.
(10)
1a
1pk0D01
D:5-78
1b
1pk0D02
D:79-146
1c
1pk0E02
E:79-146
1d
1pk0F02
F:79-146
1e
1pk0E01
E:5-78
1f
1pk0F01
F:5-78
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_Anthrax_toxA_1pk0C01 (C:293-472)
1b: PFAM_Anthrax_toxA_1pk0C02 (C:293-472)
1c: PFAM_Anthrax_toxA_1pk0C03 (C:293-472)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Anthrax_toxA]
(16)
Family
:
Anthrax_toxA
(16)
Bacillus anthracis
(13)
1a
Anthrax_toxA-1pk0C01
C:293-472
1b
Anthrax_toxA-1pk0C02
C:293-472
1c
Anthrax_toxA-1pk0C03
C:293-472
[
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]
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Asym.Unit (321 KB)
Header - Asym.Unit
Biol.Unit 1 (311 KB)
Header - Biol.Unit 1
Biol.Unit 2 (111 KB)
Header - Biol.Unit 2
Biol.Unit 3 (108 KB)
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