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2ZNE
Asym. Unit
Info
Asym.Unit (68 KB)
Biol.Unit 1 (33 KB)
Biol.Unit 2 (33 KB)
Biol.Unit 3 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ZN2+-BOUND FORM OF DES3-23ALG-2 COMPLEXED WITH ALIX ABS PEPTIDE
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
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Penta-Ef-Hand Protein, Calcium Binding Protein, Apoptosis, Endoplasmic Reticulum, Membrane, Nucleus, Polymorphism, Cytoplasm, Host-Virus Interaction, Protein Transport, Transport
(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, 10)
Info
All Hetero Components
1a: SODIUM ION (NAa)
1b: SODIUM ION (NAb)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
2
Ligand/Ion
SODIUM ION
2
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:36 , ASP A:38 , SER A:40 , VAL A:42 , GLU A:47
BINDING SITE FOR RESIDUE ZN A 991
02
AC2
SOFTWARE
ASP A:103 , ASP A:105 , SER A:107 , MET A:109 , GLU A:114 , ZN A:994
BINDING SITE FOR RESIDUE ZN A 992
03
AC3
SOFTWARE
ASP A:171 , ASP A:173 , NA A:995 , HOH A:1000 , HOH A:1018
BINDING SITE FOR RESIDUE ZN A 993
04
AC4
SOFTWARE
ASP A:105 , ASP A:111 , GLU A:114 , ZN A:992 , HOH A:1021
BINDING SITE FOR RESIDUE ZN A 994
05
AC5
SOFTWARE
ASP B:36 , ASP B:38 , SER B:40 , VAL B:42 , GLU B:47 , HOH B:1028
BINDING SITE FOR RESIDUE ZN B 991
06
AC6
SOFTWARE
ASP B:103 , ASP B:105 , SER B:107 , MET B:109 , GLU B:114 , ZN B:994
BINDING SITE FOR RESIDUE ZN B 992
07
AC7
SOFTWARE
NA B:1 , ASP B:171 , ASP B:173 , HOH B:1007 , HOH B:1017
BINDING SITE FOR RESIDUE ZN B 993
08
AC8
SOFTWARE
ASP B:105 , ASP B:111 , GLN B:145 , ZN B:992 , HOH B:995
BINDING SITE FOR RESIDUE ZN B 994
09
AC9
SOFTWARE
ASP B:169 , ASP B:171 , ASP B:173 , TRP B:175 , ZN B:993 , HOH B:1005 , HOH B:1017
BINDING SITE FOR RESIDUE NA B 1
10
BC1
SOFTWARE
ASP A:169 , ASP A:171 , ASP A:173 , TRP A:175 , ZN A:993 , HOH A:1019
BINDING SITE FOR RESIDUE NA A 995
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
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, 8)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (-|A:90-125,B:90-125|A:156-191,B:15...)
2: EF_HAND_1 (A:36-48,B:36-48|A:103-115,B:103-11...)
;
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.
PDCD6_HUMAN
23-58
90-125
156-191
4
-
A:90-125
B:90-125
A:156-191
B:156-191
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
(2, 3)
Info
All Exons
Exon 1.22b (C:2-13 | D:1-12)
Exon 1.23b (C:13-16 | -)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.21c/1.22b
2: Boundary 1.22b/1.23b
3: Boundary 1.23b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000307296
1b
ENSE00001884181
chr3:
33839844-33840429
586
PDC6I_HUMAN
1-70
70
0
-
-
1.4
ENST00000307296
4
ENSE00001770534
chr3:
33853564-33853618
55
PDC6I_HUMAN
70-88
19
0
-
-
1.5b
ENST00000307296
5b
ENSE00001632925
chr3:
33855051-33855120
70
PDC6I_HUMAN
89-112
24
0
-
-
1.6c
ENST00000307296
6c
ENSE00001802994
chr3:
33863447-33863574
128
PDC6I_HUMAN
112-154
43
0
-
-
1.7d
ENST00000307296
7d
ENSE00001141015
chr3:
33866679-33866832
154
PDC6I_HUMAN
155-206
52
0
-
-
1.8b
ENST00000307296
8b
ENSE00001141009
chr3:
33867972-33868072
101
PDC6I_HUMAN
206-239
34
0
-
-
1.10c
ENST00000307296
10c
ENSE00001141002
chr3:
33870345-33870461
117
PDC6I_HUMAN
240-278
39
0
-
-
1.12b
ENST00000307296
12b
ENSE00001608471
chr3:
33877536-33877758
223
PDC6I_HUMAN
279-353
75
0
-
-
1.13b
ENST00000307296
13b
ENSE00001630102
chr3:
33879696-33879819
124
PDC6I_HUMAN
353-394
42
0
-
-
1.14
ENST00000307296
14
ENSE00001140976
chr3:
33883389-33883566
178
PDC6I_HUMAN
394-453
60
0
-
-
1.15b
ENST00000307296
15b
ENSE00001785905
chr3:
33885604-33885715
112
PDC6I_HUMAN
454-491
38
0
-
-
1.16
ENST00000307296
16
ENSE00001732288
chr3:
33886911-33887080
170
PDC6I_HUMAN
491-547
57
0
-
-
1.18a
ENST00000307296
18a
ENSE00001783635
chr3:
33893980-33894228
249
PDC6I_HUMAN
548-630
83
0
-
-
1.19b
ENST00000307296
19b
ENSE00001596979
chr3:
33895371-33895505
135
PDC6I_HUMAN
631-675
45
0
-
-
1.20b
ENST00000307296
20b
ENSE00001097440
chr3:
33896658-33896752
95
PDC6I_HUMAN
676-707
32
0
-
-
1.21c
ENST00000307296
21c
ENSE00001140939
chr3:
33905498-33905621
124
PDC6I_HUMAN
707-748
42
0
-
-
1.22b
ENST00000307296
22b
ENSE00001140934
chr3:
33906735-33906922
188
PDC6I_HUMAN
749-811
63
2
C:2-13
D:1-12
12
12
1.23b
ENST00000307296
23b
ENSE00001218677
chr3:
33907843-33911194
3352
PDC6I_HUMAN
811-868
58
1
C:13-16
-
4
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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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, 4)
Info
all PFAM domains
1a: PFAM_EF_hand_5_2zneB01 (B:91-155)
1b: PFAM_EF_hand_5_2zneB02 (B:91-155)
2a: PFAM_EF_hand_6_2zneB03 (B:39-90)
2b: PFAM_EF_hand_6_2zneB04 (B:39-90)
View:
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Clans
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(
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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_5-2zneB01
B:91-155
1b
EF_hand_5-2zneB02
B:91-155
Family
:
EF_hand_6
(75)
Homo sapiens (Human)
(34)
2a
EF_hand_6-2zneB03
B:39-90
2b
EF_hand_6-2zneB04
B:39-90
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