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2ZND
Asym. Unit
Info
Asym.Unit (37 KB)
Biol.Unit 1 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CA2+-FREE 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
:
1.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Penta-Ef-Hand Protein, Calcium Binding Protein, Apoptosis, Calcium, 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
(3, 10)
Info
All Hetero Components
1a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
1b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
1c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
1d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
1e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MRD
5
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
2
NA
3
Ligand/Ion
SODIUM ION
3
PO4
2
Ligand/Ion
PHOSPHATE 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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:66 , SER A:70 , ASP A:73 , ASN A:76 , LYS A:77 , ALA A:78 , HOH A:307
BINDING SITE FOR RESIDUE MRD A 1
02
AC2
SOFTWARE
SER A:53 , ASN A:54 , GLY A:55 , GLN A:96 , ARG A:100 , PHE A:148
BINDING SITE FOR RESIDUE MRD A 2
03
AC3
SOFTWARE
THR A:162 , ASP A:169 , GLY A:174 , HOH A:205 , HOH A:234
BINDING SITE FOR RESIDUE MRD A 3
04
AC4
SOFTWARE
MRD A:5 , ASP A:94 , TRP A:95 , VAL A:98
BINDING SITE FOR RESIDUE MRD A 4
05
AC5
SOFTWARE
MRD A:4 , ARG A:104 , PHE A:122 , TYR A:124 , GLN A:159 , HOH A:207
BINDING SITE FOR RESIDUE MRD A 5
06
AC6
SOFTWARE
ARG A:140 , GLN A:141
BINDING SITE FOR RESIDUE PO4 A 192
07
AC7
SOFTWARE
PHE A:188 , HOH A:280
BINDING SITE FOR RESIDUE PO4 A 193
08
AC8
SOFTWARE
ASP A:36 , ASP A:38 , SER A:40 , VAL A:42 , GLU A:47 , HOH A:268
BINDING SITE FOR RESIDUE NA A 194
09
AC9
SOFTWARE
ASP A:103 , ASP A:105 , SER A:107 , MET A:109 , HOH A:221
BINDING SITE FOR RESIDUE NA A 195
10
BC1
SOFTWARE
ASP A:169 , ASP A:171 , ASP A:173 , TRP A:175 , HOH A:223 , HOH A:252
BINDING SITE FOR RESIDUE NA A 196
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035459 (G123C, chain A, )
2: VAR_PDCD6_HUMAN_CCDS3854_1_01 (G123C, chain A, )
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
G
123
C
2
CancerSNP
VAR_PDCD6_HUMAN_CCDS3854_1_01
*
G
123
C
PDCD6_HUMAN
Disease (Breast cancer)
---
A
G
123
C
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (-|A:90-125|A:156-191)
2: EF_HAND_1 (A:36-48|A: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
2
-
A:90-125
A:156-191
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
PDCD6_HUMAN
36-48
103-115
2
A:36-48
A:103-115
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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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2znda_ (A:)
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)
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)
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)
Protein Domains
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)
(
)
Organisms
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)
(
)
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
d2znda_
A:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_EF_hand_5_2zndA01 (A:91-155)
2a: PFAM_EF_hand_6_2zndA02 (A:39-90)
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Clan
:
EF_hand
(270)
Family
:
EF_hand_5
(126)
Homo sapiens (Human)
(31)
1a
EF_hand_5-2zndA01
A:91-155
Family
:
EF_hand_6
(75)
Homo sapiens (Human)
(34)
2a
EF_hand_6-2zndA02
A:39-90
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Chain A
Asymmetric Unit 1
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