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2WEL
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (84 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SU6656-BOUND CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE II DELTA IN COMPLEX WITH CALMODULIN
Authors
:
A. C. W. Pike, P. Rellos, E. Salah, N. Burgess-Brown, T. Keates, J. Muniz A. Roos, P. Filippakopoulos, F. Von Delft, A. Edwards, J. Weigelt, C. H. Arrowsmith, C. Bountra, S. Knapp
Date
:
31 Mar 09 (Deposition) - 14 Apr 09 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,D
Biol. Unit 1: A,D (1x)
Keywords
:
Cellular Differentiation, Serine/Threonine-Protein Kinase, Phosphoprotein, Calmodulin-Binding, Calmodulin Binding, Kinase, Transferase, Atp-Binding, Nucleotide-Binding, Vascular Smooth Muscle, Serine-Threonine Kinase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Rellos, A. C. W. Pike, F. H. Niesen, E. Salah, W. H. Lee, F. Von Delft, S. Knapp
Structure Of The Camkiidelta/Calmodulin Complex Reveals The Molecular Mechanism Of Camkii Kinase Activation.
Plos Biol. V. 8 426 2010
[
close entry info
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Hetero Components
(4, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: (3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7... (K88a)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
K88
1
Ligand/Ion
(3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE
4
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:20 , VAL A:28 , ALA A:41 , LYS A:43 , PHE A:90 , ASP A:91 , LEU A:92 , VAL A:93 , ASP A:157 , EDO A:700 , EDO A:701
BINDING SITE FOR RESIDUE K88 A 600
02
AC2
SOFTWARE
K88 A:600 , HOH A:2289 , HOH A:2290
BINDING SITE FOR RESIDUE EDO A 700
03
AC3
SOFTWARE
GLU A:61 , VAL A:74 , PHE A:90 , ALA A:156 , ASP A:157 , PHE A:158 , K88 A:600
BINDING SITE FOR RESIDUE EDO A 701
04
AC4
SOFTWARE
GLU A:140 , TYR A:180 , HIS A:283 , GLN A:285 , HOH A:2292
BINDING SITE FOR RESIDUE EDO A 702
05
AC5
SOFTWARE
HIS A:55 , SER A:81 , LYS A:147 , PO4 A:706
BINDING SITE FOR RESIDUE EDO A 703
06
AC6
SOFTWARE
TYR A:14 , LYS A:33 , HIS A:77 , PO4 A:707 , HOH A:2089 , HOH A:2293 , HOH D:2092
BINDING SITE FOR RESIDUE EDO A 704
07
AC7
SOFTWARE
TYR A:205 , PRO A:213 , TYR A:231 , ASP A:232 , HOH A:2294
BINDING SITE FOR RESIDUE EDO A 705
08
AC8
SOFTWARE
THR A:47 , HIS A:55 , SER A:81 , GLU A:82 , PHE A:85 , HIS A:86 , SER A:148 , LYS A:149 , EDO A:703 , HOH A:2295
BINDING SITE FOR RESIDUE PO4 A 706
09
AC9
SOFTWARE
LYS A:69 , ARG A:75 , HIS A:77 , EDO A:704 , HOH A:2089 , HOH A:2297
BINDING SITE FOR RESIDUE PO4 A 707
10
BC1
SOFTWARE
ASP D:21 , ASP D:23 , ASP D:25 , THR D:27 , GLU D:32 , HOH D:2019
BINDING SITE FOR RESIDUE CA D 600
11
BC2
SOFTWARE
ASP D:57 , ASP D:59 , ASN D:61 , THR D:63 , GLU D:68 , HOH D:2053
BINDING SITE FOR RESIDUE CA D 601
12
BC3
SOFTWARE
ASP D:94 , ASP D:96 , ASN D:98 , TYR D:100 , GLU D:105 , HOH D:2104
BINDING SITE FOR RESIDUE CA D 602
13
BC4
SOFTWARE
ASP D:130 , ASP D:132 , ASP D:134 , GLN D:136 , GLU D:141 , HOH D:2102
BINDING SITE FOR RESIDUE CA D 603
[
close Site info
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SAPs(SNPs)/Variants
(12, 12)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_069222 (N54I, chain D, )
02: VAR_048585 (M73T, chain D, )
03: VAR_073275 (F90L, chain D, )
04: VAR_073276 (D96V, chain D, )
05: VAR_073277 (N98I, chain D, )
06: VAR_069223 (N98S, chain D, )
07: VAR_073278 (D130G, chain D, )
08: VAR_073279 (D132E, chain D, )
09: VAR_073280 (D134H, chain D, )
10: VAR_073281 (Q136P, chain D, )
11: VAR_073282 (F142L, chain D, )
12: VAR_040602 (D167E, chain A, )
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
N
54
I
02
UniProt
VAR_048585
M
73
T
CALM_HUMAN
Polymorphism
41389749
D
M
73
T
03
UniProt
VAR_073275
F
90
L
CALM_HUMAN
Disease (LQT14)
---
D
F
90
L
04
UniProt
VAR_073276
D
96
V
CALM_HUMAN
Disease (LQT15)
---
D
D
96
V
05
UniProt
VAR_073277
N
98
I
CALM_HUMAN
Disease (LQT15)
---
D
N
98
I
06
UniProt
VAR_069223
N
98
S
CALM_HUMAN
Disease (CPVT4)
---
D
N
98
S
07
UniProt
VAR_073278
D
130
G
CALM_HUMAN
Disease (LQT14)
---
D
D
130
G
08
UniProt
VAR_073279
D
132
E
CALM_HUMAN
Disease (LQT15)
---
D
D
132
E
09
UniProt
VAR_073280
D
134
H
CALM_HUMAN
Disease (LQT15)
---
D
D
134
H
10
UniProt
VAR_073281
Q
136
P
CALM_HUMAN
Disease (LQT15)
---
D
Q
136
P
11
UniProt
VAR_073282
F
142
L
CALM_HUMAN
Disease (LQT14)
---
D
F
142
L
12
UniProt
VAR_040602
D
167
E
KCC2D_HUMAN
Polymorphism
35367671
A
D
167
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(4, 10)
Info
All PROSITE Patterns/Profiles
1: EF_HAND_2 (D:8-43|D:44-79|D:81-116|D:117-147,...)
2: PROTEIN_KINASE_ATP (A:20-43)
3: EF_HAND_1 (D:21-33|D:57-69|D:94-106|D:130-142...)
4: PROTEIN_KINASE_ST (A:132-144)
;
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
4
D:8-43
D:44-79
D:81-116
D:117-147
CALM2_HUMAN
8-43
44-79
81-116
117-149
4
D:8-43
D:44-79
D:81-116
D:117-147
CALM3_HUMAN
8-43
44-79
81-116
117-149
4
D:8-43
D:44-79
D:81-116
D:117-147
2
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
KCC2D_HUMAN
20-43
1
A:20-43
3
EF_HAND_1
PS00018
EF-hand calcium-binding domain.
CALM1_HUMAN
21-33
57-69
94-106
130-142
4
D:21-33
D:57-69
D:94-106
D:130-142
CALM2_HUMAN
21-33
57-69
94-106
130-142
4
D:21-33
D:57-69
D:94-106
D:130-142
CALM3_HUMAN
21-33
57-69
94-106
130-142
4
D:21-33
D:57-69
D:94-106
D:130-142
4
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
KCC2D_HUMAN
132-144
1
A:132-144
[
close PROSITE info
]
Exons
(13, 13)
Info
All Exons
Exon 1.1i (A:-1-22)
Exon 1.2a (A:22-54)
Exon 1.4 (A:54-74)
Exon 1.5 (A:74-92)
Exon 1.6 (A:92-114)
Exon 1.7 (A:114-138)
Exon 1.9 (A:139-173)
Exon 1.10 (A:173-201)
Exon 1.11a (A:201-232)
Exon 1.12 (A:233-273)
Exon 1.13a (A:274-301 (gaps))
Exon 1.14 (A:302-316)
Exon 1.15a (A:316-316)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1i
02: Boundary 1.1i/1.2a
03: Boundary 1.2a/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11a
10: Boundary 1.11a/1.12
11: Boundary 1.12/1.13a
12: Boundary 1.13a/1.14
13: Boundary 1.14/1.15a
14: Boundary 1.15a/1.19a
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
1.1i
ENST00000342666
1i
ENSE00001872886
chr4:
114682224-114682160
65
KCC2D_HUMAN
1-22
22
1
A:-1-22
14
1.2a
ENST00000342666
2a
ENSE00001679875
chr4:
114680570-114680476
95
KCC2D_HUMAN
22-54
33
1
A:22-54
33
1.4
ENST00000342666
4
ENSE00001795805
chr4:
114582928-114582869
60
KCC2D_HUMAN
54-74
21
1
A:54-74
21
1.5
ENST00000342666
5
ENSE00001276352
chr4:
114530362-114530308
55
KCC2D_HUMAN
74-92
19
1
A:74-92
19
1.6
ENST00000342666
6
ENSE00001003913
chr4:
114473252-114473187
66
KCC2D_HUMAN
92-114
23
1
A:92-114
23
1.7
ENST00000342666
7
ENSE00001276336
chr4:
114469885-114469813
73
KCC2D_HUMAN
114-138
25
1
A:114-138
25
1.9
ENST00000342666
9
ENSE00001617342
chr4:
114458599-114458497
103
KCC2D_HUMAN
139-173
35
1
A:139-173
35
1.10
ENST00000342666
10
ENSE00001672540
chr4:
114452455-114452372
84
KCC2D_HUMAN
173-201
29
1
A:173-201
29
1.11a
ENST00000342666
11a
ENSE00001699970
chr4:
114438813-114438719
95
KCC2D_HUMAN
201-232
32
1
A:201-232
32
1.12
ENST00000342666
12
ENSE00001003911
chr4:
114436347-114436225
123
KCC2D_HUMAN
233-273
41
1
A:233-273
41
1.13a
ENST00000342666
13a
ENSE00001791998
chr4:
114435069-114434986
84
KCC2D_HUMAN
274-301
28
1
A:274-301 (gaps)
28
1.14
ENST00000342666
14
ENSE00001752494
chr4:
114434526-114434484
43
KCC2D_HUMAN
302-316
15
1
A:302-316
15
1.15a
ENST00000342666
15a
ENSE00001121166
chr4:
114430831-114430794
38
KCC2D_HUMAN
316-328
13
1
A:316-316
1
1.19a
ENST00000342666
19a
ENSE00001003903
chr4:
114421667-114421619
49
KCC2D_HUMAN
329-345
17
0
-
-
1.20
ENST00000342666
20
ENSE00001121155
chr4:
114386760-114386685
76
KCC2D_HUMAN
345-370
26
0
-
-
1.21
ENST00000342666
21
ENSE00002169632
chr4:
114381397-114381303
95
KCC2D_HUMAN
370-402
33
0
-
-
1.22a
ENST00000342666
22a
ENSE00001276264
chr4:
114378719-114378491
229
KCC2D_HUMAN
402-478
77
0
-
-
1.23b
ENST00000342666
23b
ENSE00001276388
chr4:
114376977-114376882
96
KCC2D_HUMAN
478-499
22
0
-
-
1.24a
ENST00000342666
24a
ENSE00002033536
chr4:
114375671-114375261
411
KCC2D_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d2weld_ (D:)
2a: SCOP_d2wela_ (A:)
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Protein Domains
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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
d2weld_
D:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
automated matches
(529)
Protein domain
:
automated matches
(529)
Human (Homo sapiens) [TaxId: 9606]
(438)
2a
d2wela_
A:
[
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2welA02 (A:94-276)
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Organisms
(
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(
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Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
1a
2welA02
A:94-276
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Pkinase_2welA01 (A:14-272)
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Clans
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(
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(
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(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-2welA01
A:14-272
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