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2VN9
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (51 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE II DELTA ISOFORM 1, CAMKD
Authors
:
A. K. Roos, P. Rellos, E. Salah, A. C. W. Pike, O. Fedorov, E. S. Pilka, F. V C. H. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, S. Knapp
Date
:
31 Jan 08 (Deposition) - 26 Feb 08 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Serine/Threonine-Protein Kinase, Serine-Threonine Kinase, Cellular Differentiation, Vascular Smooth Muscle, Kinase, Transferase, Atp-Binding, Phosphoprotein, Calmodulin-Binding, Nucleotide-Binding
(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
[
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINEETH... (EPEa)
3a: [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-... (GVDa)
3b: [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-... (GVDb)
4a: PHOSPHATE ION (PO4a)
4b: PHOSPHATE ION (PO4b)
4c: PHOSPHATE ION (PO4c)
4d: PHOSPHATE ION (PO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3
GVD
2
Ligand/Ion
[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
4
PO4
4
Ligand/Ion
PHOSPHATE ION
[
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Sites
(8, 8)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU B:20 , LYS B:22 , ALA B:41 , LYS B:43 , ASP B:91 , LEU B:92 , VAL B:93 , ASP B:157 , PO4 B:1312
BINDING SITE FOR RESIDUE GVD B1310
2
AC2
SOFTWARE
LEU A:20 , LYS A:22 , VAL A:28 , ALA A:41 , LYS A:43 , PHE A:90 , ASP A:91 , LEU A:92 , VAL A:93 , ASP A:157 , PO4 A:1311
BINDING SITE FOR RESIDUE GVD A1314
3
AC3
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 , HOH A:2072
BINDING SITE FOR RESIDUE PO4 A1310
4
AC4
SOFTWARE
THR B:47 , HIS B:55 , SER B:81 , GLU B:82 , PHE B:85 , HIS B:86 , SER B:148 , LYS B:149
BINDING SITE FOR RESIDUE PO4 B1311
5
AC5
SOFTWARE
LEU B:20 , GVD B:1310
BINDING SITE FOR RESIDUE PO4 B1312
6
AC6
SOFTWARE
LEU A:20 , GLY A:21 , GVD A:1314 , HOH A:2073
BINDING SITE FOR RESIDUE PO4 A1311
7
AC7
SOFTWARE
ARG A:75 , HIS A:77
BINDING SITE FOR RESIDUE CL A1312
8
AC8
SOFTWARE
TYR A:107 , SER A:109 , ALA A:111 , ASP A:112 , ARG A:275 , SER A:276 , MET A:281 , HOH A:2029
BINDING SITE FOR RESIDUE EPE A1313
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_040602 (D167E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_040602
D
167
E
KCC2D_HUMAN
Polymorphism
35367671
A/B
D
167
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:20-43,B:20-43)
2: PROTEIN_KINASE_ST (A:132-144,B:132-144)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
KCC2D_HUMAN
20-43
2
A:20-43
B:20-43
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
KCC2D_HUMAN
132-144
2
A:132-144
B:132-144
[
close PROSITE info
]
Exons
(12, 24)
Info
All Exons
Exon 1.1i (A:-1-22 | B:-1-22)
Exon 1.2a (A:22-54 | B:22-54)
Exon 1.4 (A:54-74 | B:54-74)
Exon 1.5 (A:74-92 | B:74-92)
Exon 1.6 (A:92-114 | B:92-114)
Exon 1.7 (A:114-138 | B:114-138)
Exon 1.9 (A:139-173 | B:139-173)
Exon 1.10 (A:173-201 | B:173-201)
Exon 1.11a (A:201-232 | B:201-232)
Exon 1.12 (A:233-273 | B:233-273)
Exon 1.13a (A:274-301 | B:274-301)
Exon 1.14 (A:302-309 | B:302-309)
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
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
2
A:-1-22
B:-1-22
14
14
1.2a
ENST00000342666
2a
ENSE00001679875
chr4:
114680570-114680476
95
KCC2D_HUMAN
22-54
33
2
A:22-54
B:22-54
33
33
1.4
ENST00000342666
4
ENSE00001795805
chr4:
114582928-114582869
60
KCC2D_HUMAN
54-74
21
2
A:54-74
B:54-74
21
21
1.5
ENST00000342666
5
ENSE00001276352
chr4:
114530362-114530308
55
KCC2D_HUMAN
74-92
19
2
A:74-92
B:74-92
19
19
1.6
ENST00000342666
6
ENSE00001003913
chr4:
114473252-114473187
66
KCC2D_HUMAN
92-114
23
2
A:92-114
B:92-114
23
23
1.7
ENST00000342666
7
ENSE00001276336
chr4:
114469885-114469813
73
KCC2D_HUMAN
114-138
25
2
A:114-138
B:114-138
25
25
1.9
ENST00000342666
9
ENSE00001617342
chr4:
114458599-114458497
103
KCC2D_HUMAN
139-173
35
2
A:139-173
B:139-173
35
35
1.10
ENST00000342666
10
ENSE00001672540
chr4:
114452455-114452372
84
KCC2D_HUMAN
173-201
29
2
A:173-201
B:173-201
29
29
1.11a
ENST00000342666
11a
ENSE00001699970
chr4:
114438813-114438719
95
KCC2D_HUMAN
201-232
32
2
A:201-232
B:201-232
32
32
1.12
ENST00000342666
12
ENSE00001003911
chr4:
114436347-114436225
123
KCC2D_HUMAN
233-273
41
2
A:233-273
B:233-273
41
41
1.13a
ENST00000342666
13a
ENSE00001791998
chr4:
114435069-114434986
84
KCC2D_HUMAN
274-301
28
2
A:274-301
B:274-301
28
28
1.14
ENST00000342666
14
ENSE00001752494
chr4:
114434526-114434484
43
KCC2D_HUMAN
302-316
15
2
A:302-309
B:302-309
8
8
1.15a
ENST00000342666
15a
ENSE00001121166
chr4:
114430831-114430794
38
KCC2D_HUMAN
316-328
13
0
-
-
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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2vn9a_ (A:)
1b: SCOP_d2vn9b_ (B:)
View:
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Classes
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)
(
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Folds
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d2vn9a_
A:
1b
d2vn9b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2vn9A02 (A:93-309)
1b: CATH_2vn9B02 (B:93-309)
View:
Select:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
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
2vn9A02
A:93-309
1b
2vn9B02
B:93-309
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pkinase_2vn9B01 (B:14-272)
1b: PFAM_Pkinase_2vn9B02 (B:14-272)
View:
Select:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-2vn9B01
B:14-272
1b
Pkinase-2vn9B02
B:14-272
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