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2ZRS
Asym. Unit
Info
Asym.Unit (225 KB)
Biol.Unit 1 (57 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (58 KB)
Biol.Unit 4 (57 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CA2+-BOUND FORM OF DES3-23ALG-2
Authors
:
H. Suzuki, M. Kawasaki, T. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki
Date
:
01 Sep 08 (Deposition) - 04 Nov 08 (Release) - 09 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
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. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki
Crystallization And X-Ray Diffraction Analysis Of N-Terminally Truncated Human Alg-2
Acta Crystallogr. , Sect. F V. 64 974 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 25)
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)
1s: CALCIUM ION (CAs)
1t: CALCIUM ION (CAt)
1u: CALCIUM ION (CAu)
1v: CALCIUM ION (CAv)
1w: CALCIUM ION (CAw)
1x: CALCIUM ION (CAx)
1y: CALCIUM ION (CAy)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
25
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:103 , ARG A:104 , ASP A:105 , MET A:109 , GLU A:114
BINDING SITE FOR RESIDUE CA A 990
02
AC2
SOFTWARE
SER A:40 , GLY A:41 , GLU A:47
BINDING SITE FOR RESIDUE CA A 991
03
AC3
SOFTWARE
ASP B:103 , ASP B:105 , ASN B:106 , SER B:107 , MET B:109 , GLU B:114
BINDING SITE FOR RESIDUE CA B 990
04
AC4
SOFTWARE
ASP B:169 , THR B:170 , ASP B:171 , TRP B:175
BINDING SITE FOR RESIDUE CA B 991
05
AC5
SOFTWARE
ASP B:36 , ASP B:38 , SER B:40 , SER B:44 , GLU B:47
BINDING SITE FOR RESIDUE CA B 992
06
AC6
SOFTWARE
ASP C:36 , ASP C:38 , GLU C:47
BINDING SITE FOR RESIDUE CA C 990
07
AC7
SOFTWARE
ASP C:105 , SER C:107 , MET C:109
BINDING SITE FOR RESIDUE CA C 991
08
AC8
SOFTWARE
ASP C:169 , ASP C:173 , TRP C:175
BINDING SITE FOR RESIDUE CA C 992
09
AC9
SOFTWARE
ASP D:36 , ASP D:38 , SER D:40 , SER D:44 , GLU D:47
BINDING SITE FOR RESIDUE CA D 990
10
BC1
SOFTWARE
ASP D:103 , ASP D:105 , SER D:107 , MET D:109 , GLU D:114
BINDING SITE FOR RESIDUE CA D 991
11
BC2
SOFTWARE
ASP D:169 , ASP D:171 , ASP D:173 , ILE D:176
BINDING SITE FOR RESIDUE CA D 992
12
BC3
SOFTWARE
ASP E:36 , ASP E:38 , SER E:40 , GLU E:47
BINDING SITE FOR RESIDUE CA E 990
13
BC4
SOFTWARE
ASP E:103 , ASP E:105 , SER E:107 , MET E:109 , ILE E:110 , GLU E:114
BINDING SITE FOR RESIDUE CA E 991
14
BC5
SOFTWARE
ASP E:169 , ASP E:173 , TRP E:175 , ILE E:176
BINDING SITE FOR RESIDUE CA E 992
15
BC6
SOFTWARE
ASP F:36 , SER F:40 , GLU F:47
BINDING SITE FOR RESIDUE CA F 990
16
BC7
SOFTWARE
ASP F:103 , ASP F:105 , SER F:107 , MET F:109 , GLU F:114
BINDING SITE FOR RESIDUE CA F 991
17
BC8
SOFTWARE
ASP F:169 , ASP F:171 , ASP F:173 , TRP F:175 , ILE F:176
BINDING SITE FOR RESIDUE CA F 992
18
BC9
SOFTWARE
ASP G:36 , ASP G:38 , SER G:40 , GLU G:47
BINDING SITE FOR RESIDUE CA G 990
19
CC1
SOFTWARE
ASP G:103 , ASP G:105 , SER G:107 , GLY G:108 , MET G:109 , GLU G:114
BINDING SITE FOR RESIDUE CA G 991
20
CC2
SOFTWARE
TRP G:175 , ILE G:176
BINDING SITE FOR RESIDUE CA G 992
21
CC3
SOFTWARE
ASP H:36 , SER H:40 , GLU H:47
BINDING SITE FOR RESIDUE CA H 990
22
CC4
SOFTWARE
ASP H:103 , SER H:107 , GLY H:108 , MET H:109
BINDING SITE FOR RESIDUE CA H 991
23
CC5
SOFTWARE
TYR H:168 , ASP H:169 , THR H:170 , ASP H:173 , TRP H:175
BINDING SITE FOR RESIDUE CA H 992
24
CC6
SOFTWARE
ASN F:106 , ASN G:106
BINDING SITE FOR RESIDUE CA G 1
25
CC7
SOFTWARE
ASN B:106 , ASN C:106
BINDING SITE FOR RESIDUE CA B 2
[
close Site info
]
SAPs(SNPs)/Variants
(2, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035459 (G123C, chain A/B/C/D/E/F/G/H, )
2: VAR_PDCD6_HUMAN_CCDS3854_1_01 (G123C, chain A/B/C/D/E/F/G/H, )
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/C/D/E/F/G/H
G
123
C
2
CancerSNP
VAR_PDCD6_HUMAN_CCDS3854_1_01
*
G
123
C
PDCD6_HUMAN
Disease (Breast cancer)
---
A/B/C/D/E/F/G/H
G
123
C
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 32)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (-|A:90-125,B:90-125,C:90-125,D:90-...)
2: EF_HAND_1 (A:36-48,B:36-48,C:36-48,D:36-48,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.
PDCD6_HUMAN
23-58
90-125
156-191
16
-
A:90-125
B:90-125
C:90-125
D:90-125
E:90-125
F:90-125
G:90-125
H:90-125
A:156-188
B:156-188
C:156-188
D:156-188
E:156-189
F:156-188
G:156-188
H:156-188
2
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
PDCD6_HUMAN
36-48
103-115
16
A:36-48
B:36-48
C:36-48
D:36-48
E:36-48
F:36-48
G:36-48
H:36-48
A:103-115
B:103-115
C:103-115
D:103-115
E:103-115
F:103-115
G:103-115
H:103-115
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2zrsa_ (A:)
1b: SCOP_d2zrsb_ (B:)
1c: SCOP_d2zrsc_ (C:)
1d: SCOP_d2zrsd_ (D:)
1e: SCOP_d2zrse_ (E:)
1f: SCOP_d2zrsf_ (F:)
1g: SCOP_d2zrsg_ (G:)
1h: SCOP_d2zrsh_ (H:)
View:
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Classes
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Protein Domains
(
)
(
)
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
d2zrsa_
A:
1b
d2zrsb_
B:
1c
d2zrsc_
C:
1d
d2zrsd_
D:
1e
d2zrse_
E:
1f
d2zrsf_
F:
1g
d2zrsg_
G:
1h
d2zrsh_
H:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 16)
Info
all PFAM domains
1a: PFAM_EF_hand_5_2zrsH01 (H:91-155)
1b: PFAM_EF_hand_5_2zrsH02 (H:91-155)
1c: PFAM_EF_hand_5_2zrsH03 (H:91-155)
1d: PFAM_EF_hand_5_2zrsH04 (H:91-155)
1e: PFAM_EF_hand_5_2zrsH05 (H:91-155)
1f: PFAM_EF_hand_5_2zrsH06 (H:91-155)
1g: PFAM_EF_hand_5_2zrsH07 (H:91-155)
1h: PFAM_EF_hand_5_2zrsH08 (H:91-155)
2a: PFAM_EF_hand_6_2zrsH09 (H:39-90)
2b: PFAM_EF_hand_6_2zrsH10 (H:39-90)
2c: PFAM_EF_hand_6_2zrsH11 (H:39-90)
2d: PFAM_EF_hand_6_2zrsH12 (H:39-90)
2e: PFAM_EF_hand_6_2zrsH13 (H:39-90)
2f: PFAM_EF_hand_6_2zrsH14 (H:39-90)
2g: PFAM_EF_hand_6_2zrsH15 (H:39-90)
2h: PFAM_EF_hand_6_2zrsH16 (H:39-90)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EF_hand
(270)
Family
:
EF_hand_5
(126)
Homo sapiens (Human)
(31)
1a
EF_hand_5-2zrsH01
H:91-155
1b
EF_hand_5-2zrsH02
H:91-155
1c
EF_hand_5-2zrsH03
H:91-155
1d
EF_hand_5-2zrsH04
H:91-155
1e
EF_hand_5-2zrsH05
H:91-155
1f
EF_hand_5-2zrsH06
H:91-155
1g
EF_hand_5-2zrsH07
H:91-155
1h
EF_hand_5-2zrsH08
H:91-155
Family
:
EF_hand_6
(75)
Homo sapiens (Human)
(34)
2a
EF_hand_6-2zrsH09
H:39-90
2b
EF_hand_6-2zrsH10
H:39-90
2c
EF_hand_6-2zrsH11
H:39-90
2d
EF_hand_6-2zrsH12
H:39-90
2e
EF_hand_6-2zrsH13
H:39-90
2f
EF_hand_6-2zrsH14
H:39-90
2g
EF_hand_6-2zrsH15
H:39-90
2h
EF_hand_6-2zrsH16
H:39-90
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