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3BQR
Asym. Unit
Info
Asym.Unit (58 KB)
Biol.Unit 1 (104 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3) IN COMPLEX WITH AN IMIDAZO-PYRIDAZINE LIGAND
Authors
:
P. Filippakopoulos, P. Rellos, O. Fedorov, F. Niesen, A. C. W. Pike, E. S F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, S. Knapp, St Genomics Consortium (Sgc)
Date
:
20 Dec 07 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Death Associated Kinase, Dapk3, Zip Kinase, Zipk, Dap Kinase 3, Dap Like Kinase, Dlk, Structural Genomics Consortium, Sgc, Apoptosis, Atp-Binding, Chromatin Regulator, Nucleotide-Binding, Nucleus, Serine/Threonine-Protein Kinase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Filippakopoulos, P. Rellos, O. Fedorov, F. Niesen, A. C. W. Pike, E. S. Pilka, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, S. Knapp
Crystal Structure Of Human Death Associated Protein Kinase (Dapk3) In Complex With An Imidazo-Pyridazine Ligand.
To Be Published
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPY... (4RBa)
2a: GLYCEROL (GOLa)
3a: S-1,2-PROPANEDIOL (PGOa)
3b: S-1,2-PROPANEDIOL (PGOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4RB
1
Ligand/Ion
4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZOIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
PGO
2
Ligand/Ion
S-1,2-PROPANEDIOL
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:20 , ALA A:40 , LYS A:42 , GLU A:94 , LEU A:95 , GLU A:100 , MET A:146 , ILE A:160 , ASP A:161 , HOH A:588 , HOH A:632 , HOH A:637 , HOH A:656
BINDING SITE FOR RESIDUE 4RB A 401
2
AC2
SOFTWARE
ARG A:69 , ASP A:81
BINDING SITE FOR RESIDUE PGO A 501
3
AC3
SOFTWARE
TYR A:234 , PHE A:236 , ARG A:253
BINDING SITE FOR RESIDUE PGO A 502
4
AC4
SOFTWARE
LYS A:42 , ILE A:44 , GLU A:64 , ASP A:161 , HOH A:689 , HOH A:779
BINDING SITE FOR RESIDUE GOL A 503
[
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SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_040438 (T112M, chain A, )
2: VAR_040439 (D161N, chain A, )
3: VAR_040440 (P216S, chain A, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_040438
T
112
M
DAPK3_HUMAN
Unclassified
---
A
T
112
M
2
UniProt
VAR_040439
D
161
N
DAPK3_HUMAN
Unclassified
---
A
D
161
N
3
UniProt
VAR_040440
P
216
S
DAPK3_HUMAN
Unclassified
---
A
P
216
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:19-46)
2: PROTEIN_KINASE_ST (A:135-147)
;
View:
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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.
DAPK3_HUMAN
19-46
1
A:19-46
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
DAPK3_HUMAN
135-147
1
A:135-147
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Exons
(8, 8)
Info
All Exons
Exon 1.1 (A:7-21)
Exon 1.2 (A:21-141)
Exon 1.3 (A:142-185 (gaps))
Exon 1.4 (A:185-201)
Exon 1.5 (A:201-210)
Exon 1.6 (A:210-261)
Exon 1.7 (A:261-276)
Exon 1.8b (A:277-284)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8b
9: Boundary 1.8b/-
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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
1.1
ENST00000301264
1
ENSE00002166557
chr19:
3969826-3969672
155
DAPK3_HUMAN
1-21
21
1
A:7-21
15
1.2
ENST00000301264
2
ENSE00001643526
chr19:
3964989-3964629
361
DAPK3_HUMAN
21-141
121
1
A:21-141
121
1.3
ENST00000301264
3
ENSE00001806720
chr19:
3964371-3964242
130
DAPK3_HUMAN
142-185
44
1
A:142-185 (gaps)
44
1.4
ENST00000301264
4
ENSE00001115355
chr19:
3963917-3963869
49
DAPK3_HUMAN
185-201
17
1
A:185-201
17
1.5
ENST00000301264
5
ENSE00001115354
chr19:
3963667-3963641
27
DAPK3_HUMAN
201-210
10
1
A:201-210
10
1.6
ENST00000301264
6
ENSE00001115351
chr19:
3961159-3961007
153
DAPK3_HUMAN
210-261
52
1
A:210-261
52
1.7
ENST00000301264
7
ENSE00001115349
chr19:
3960102-3960057
46
DAPK3_HUMAN
261-276
16
1
A:261-276
16
1.8b
ENST00000301264
8b
ENSE00001267404
chr19:
3959635-3958452
1184
DAPK3_HUMAN
277-454
178
1
A:277-284
8
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3bqra_ (A:)
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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
d3bqra_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3bqrA02 (A:99-284)
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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
3bqrA02
A:99-284
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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