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2ZN9
Biol. Unit 1
Info
Asym.Unit (64 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CA2+-BOUND FORM OF DES3-20ALG-2
Authors
:
H. Suzuki, M. Kawasaki, T. Inuzuka, T. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki
Date
:
22 Apr 08 (Deposition) - 09 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Penta-Ef-Hand Protein, Calcium Binding Protein, Apoptosis, Endoplasmic Reticulum, Membrane, Nucleus, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Suzuki, M. Kawasaki, T. Inuzuka, M. Okumura, T. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki
Structural Basis For Ca(2+)-Dependent Formation Of Alg-2/Alix Peptide Complex: Ca(2+)/Ef3-Driven Arginine Switch Mechanism
Structure V. 16 1562 2008
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: DODECAETHYLENE GLYCOL (12Pa)
2a: NONAETHYLENE GLYCOL (2PEa)
3a: CALCIUM ION (CAa)
3b: CALCIUM ION (CAb)
3c: CALCIUM ION (CAc)
3d: CALCIUM ION (CAd)
3e: CALCIUM ION (CAe)
3f: CALCIUM ION (CAf)
3g: CALCIUM ION (CAg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
12P
1
Ligand/Ion
DODECAETHYLENE GLYCOL
2
2PE
1
Ligand/Ion
NONAETHYLENE GLYCOL
3
CA
-1
Ligand/Ion
CALCIUM ION
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:36 , ASP A:38 , SER A:40 , VAL A:42 , GLU A:47 , HOH A:927
BINDING SITE FOR RESIDUE CA A 901
2
AC2
SOFTWARE
ASP A:103 , ASP A:105 , SER A:107 , MET A:109 , GLU A:114
BINDING SITE FOR RESIDUE CA A 902
3
AC3
SOFTWARE
ASP A:169 , ASP A:171 , ASP A:173 , TRP A:175 , HOH A:924 , HOH A:928
BINDING SITE FOR RESIDUE CA A 903
4
AC4
SOFTWARE
ASN A:106 , HOH A:920 , ASN B:106 , HOH B:924
BINDING SITE FOR RESIDUE CA A 904
5
AC5
SOFTWARE
TYR A:91 , TRP A:95 , PHE A:122 , GLY A:123 , TYR A:124 , ARG A:166 , PRO B:23 , GLN B:25
BINDING SITE FOR RESIDUE 2PE A 1
6
AC6
SOFTWARE
ASP B:36 , ASP B:38 , SER B:40 , VAL B:42 , GLU B:47 , HOH B:915
BINDING SITE FOR RESIDUE CA B 901
7
AC7
SOFTWARE
ASP B:103 , ASP B:105 , SER B:107 , MET B:109 , GLU B:114
BINDING SITE FOR RESIDUE CA B 902
8
AC8
SOFTWARE
ASP B:169 , ASP B:171 , ASP B:173 , TRP B:175 , HOH B:914 , HOH B:925
BINDING SITE FOR RESIDUE CA B 903
9
AC9
SOFTWARE
ALA A:21 , PRO A:23 , GLN A:25 , LEU A:28 , THR A:86 , TYR B:91 , ASP B:94 , TRP B:95 , GLY B:123 , TYR B:124 , ARG B:166
BINDING SITE FOR RESIDUE 12P B 2
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_035459 (G123C, chain A/B, )
2: VAR_PDCD6_HUMAN_CCDS3854_1_01 (G123C, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035459
G
123
C
PDCD6_HUMAN
Unclassified
---
A/B
G
123
C
2
CancerSNP
VAR_PDCD6_HUMAN_CCDS3854_1_01
*
G
123
C
PDCD6_HUMAN
Disease (Breast cancer)
---
A/B
G
123
C
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 10)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (A:23-58,A:90-125,A:156-189,B:156-1...)
2: EF_HAND_1 (A:36-48,A:103-115,B:103-115)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EF_HAND_2
PS50222
EF-hand calcium-binding domain profile.
PDCD6_HUMAN
23-58
90-125
156-191
6
A:23-58
B:23-58
A:90-125
B:90-125
A:156-189
B:156-190
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
PDCD6_HUMAN
36-48
103-115
4
A:36-48
B:36-48
A:103-115
B:103-115
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Exons
(0, 0)
Info
All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d2zn9a_ (A:)
1b: SCOP_d2zn9b_ (B:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
EF Hand-like
(739)
Superfamily
:
EF-hand
(657)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Human (Homo sapiens) [TaxId: 9606]
(35)
1a
d2zn9a_
A:
1b
d2zn9b_
B:
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_EF_hand_5_2zn9B01 (B:91-155)
1b: PFAM_EF_hand_5_2zn9B02 (B:91-155)
2a: PFAM_EF_hand_6_2zn9B03 (B:39-90)
2b: PFAM_EF_hand_6_2zn9B04 (B:39-90)
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Organisms
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(
)
Clan
:
EF_hand
(270)
Family
:
EF_hand_5
(126)
Homo sapiens (Human)
(31)
1a
EF_hand_5-2zn9B01
B:91-155
1b
EF_hand_5-2zn9B02
B:91-155
Family
:
EF_hand_6
(75)
Homo sapiens (Human)
(34)
2a
EF_hand_6-2zn9B03
B:39-90
2b
EF_hand_6-2zn9B04
B:39-90
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Asymmetric Unit 1
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Asym.Unit (64 KB)
Header - Asym.Unit
Biol.Unit 1 (60 KB)
Header - Biol.Unit 1
Biol.Unit 2 (60 KB)
Header - Biol.Unit 2
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