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3R0T
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (124 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 ALPHA SUBUNIT IN COMPLEX WITH THE INHIBITOR CX-5279
Authors
:
R. Battistutta, E. Papinutto, G. Lolli, F. Pierre, M. Haddach, D. M. Ryc
Date
:
09 Mar 11 (Deposition) - 07 Dec 11 (Release) - 29 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Kinase, Ck2-Inhibitor Complex, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Battistutta, G. Cozza, F. Pierre, E. Papinutto, G. Lolli, S. Sarno, S. E. O'Brien, A. Siddiqui-Jain, M. Haddach, K. Anderes, D. M. Ryckman F. Meggio, L. A. Pinna
Unprecedented Selectivity And Structural Determinants Of A New Class Of Protein Kinase Ck2 Inhibitors In Clinical Trials For The Treatment Of Cancer.
Biochemistry V. 50 8478 2011
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 15)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
2a: 3-(CYCLOPROPYLAMINO)-5-{[3-(TRIFLU... (FU9a)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
2
FU9
1
Ligand/Ion
3-(CYCLOPROPYLAMINO)-5-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}PYRIMIDO[4,5-C]QUINOLINE-8-CARBOXYLICACID
3
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
SO4
4
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:45 , GLY A:46 , ARG A:47 , VAL A:53 , VAL A:66 , LYS A:68 , PHE A:113 , GLU A:114 , HIS A:115 , VAL A:116 , ASN A:118 , MET A:163 , ILE A:174 , ASP A:175 , EDO A:345 , EDO A:351 , HOH A:370 , HOH A:381 , HOH A:616 , HOH A:636
BINDING SITE FOR RESIDUE FU9 A 338
02
AC2
SOFTWARE
ARG A:80 , ARG A:155 , ASN A:189 , VAL A:192 , HOH A:369 , HOH A:677
BINDING SITE FOR RESIDUE SO4 A 339
03
AC3
SOFTWARE
ARG A:191 , LYS A:198 , ASN A:238 , PEG A:343
BINDING SITE FOR RESIDUE SO4 A 340
04
AC4
SOFTWARE
ASP A:253 , ARG A:278 , ARG A:306 , TYR A:307 , ASP A:308 , HOH A:397 , HOH A:442 , HOH A:465
BINDING SITE FOR RESIDUE SO4 A 341
05
AC5
SOFTWARE
LYS A:170 , ARG A:172 , HOH A:428 , HOH A:463 , HOH A:649
BINDING SITE FOR RESIDUE SO4 A 342
06
AC6
SOFTWARE
SER A:194 , ARG A:195 , TYR A:196 , SO4 A:340 , HOH A:433 , HOH A:619
BINDING SITE FOR RESIDUE PEG A 343
07
AC7
SOFTWARE
GLN A:36 , TYR A:39 , VAL A:101 , ASP A:103 , PRO A:104 , ARG A:280
BINDING SITE FOR RESIDUE EDO A 344
08
AC8
SOFTWARE
ASN A:118 , ASP A:120 , HIS A:160 , FU9 A:338 , EDO A:348 , EDO A:351
BINDING SITE FOR RESIDUE EDO A 345
09
AC9
SOFTWARE
ASP A:37 , PRO A:295 , HIS A:321 , HOH A:620
BINDING SITE FOR RESIDUE EDO A 346
10
BC1
SOFTWARE
PHE A:232 , HOH A:372 , HOH A:573 , HOH A:621 , HOH A:668
BINDING SITE FOR RESIDUE EDO A 347
11
BC2
SOFTWARE
ASN A:118 , THR A:119 , ASP A:120 , PHE A:121 , PRO A:159 , VAL A:162 , MET A:163 , ILE A:164 , EDO A:345
BINDING SITE FOR RESIDUE EDO A 348
12
BC3
SOFTWARE
LYS A:158 , HIS A:160 , SER A:194 , EDO A:350 , HOH A:618 , HOH A:619
BINDING SITE FOR RESIDUE EDO A 349
13
BC4
SOFTWARE
PRO A:159 , PHE A:197 , GLU A:230 , EDO A:349 , HOH A:618
BINDING SITE FOR RESIDUE EDO A 350
14
BC5
SOFTWARE
ASN A:118 , FU9 A:338 , EDO A:345 , HOH A:455 , HOH A:575
BINDING SITE FOR RESIDUE EDO A 351
15
BC6
SOFTWARE
PRO A:104 , ARG A:278 , LYS A:279 , ASP A:302 , HOH A:531 , HOH A:642 , HOH A:679
BINDING SITE FOR RESIDUE EDO A 352
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_077045 (R47Q, chain A, )
2: VAR_077046 (Y50S, chain A, )
3: VAR_077047 (D175G, chain A, )
4: VAR_077048 (K198R, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_077045
R
47
Q
CSK21_HUMAN
Disease (OCNDS)
869312845
A
R
47
Q
2
UniProt
VAR_077046
Y
50
S
CSK21_HUMAN
Disease (OCNDS)
869312849
A
Y
50
S
3
UniProt
VAR_077047
D
175
G
CSK21_HUMAN
Disease (OCNDS)
869312848
A
D
175
G
4
UniProt
VAR_077048
K
198
R
CSK21_HUMAN
Disease (OCNDS)
869312840
A
K
198
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:45-68)
2: PROTEIN_KINASE_ST (A:152-164)
;
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.
CSK21_HUMAN
45-68
1
A:45-68
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CSK21_HUMAN
152-164
1
A:152-164
[
close PROSITE info
]
Exons
(11, 11)
Info
All Exons
Exon 1.3 (A:3-34)
Exon 1.4 (A:34-71)
Exon 1.5 (A:72-105)
Exon 1.6 (A:106-122)
Exon 1.7 (A:123-142)
Exon 1.8 (A:143-170)
Exon 1.9 (A:171-207)
Exon 1.10 (A:208-241)
Exon 1.11b (A:242-275)
Exon 1.12 (A:275-325)
Exon 1.13 (A:325-329)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11b
10: Boundary 1.11b/1.12
11: Boundary 1.12/1.13
12: Boundary 1.13/1.14c
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
ENST00000349736
1b
ENSE00001937660
chr20:
524465-524316
150
CSK21_HUMAN
-
0
0
-
-
1.3
ENST00000349736
3
ENSE00001709328
chr20:
489304-489095
210
CSK21_HUMAN
1-34
34
1
A:3-34
32
1.4
ENST00000349736
4
ENSE00001688643
chr20:
485873-485762
112
CSK21_HUMAN
34-71
38
1
A:34-71
38
1.5
ENST00000349736
5
ENSE00001705871
chr20:
480578-480477
102
CSK21_HUMAN
72-105
34
1
A:72-105
34
1.6
ENST00000349736
6
ENSE00001598088
chr20:
479949-479899
51
CSK21_HUMAN
106-122
17
1
A:106-122
17
1.7
ENST00000349736
7
ENSE00001618963
chr20:
478424-478365
60
CSK21_HUMAN
123-142
20
1
A:123-142
20
1.8
ENST00000349736
8
ENSE00000655095
chr20:
476446-476363
84
CSK21_HUMAN
143-170
28
1
A:143-170
28
1.9
ENST00000349736
9
ENSE00000655092
chr20:
473008-472898
111
CSK21_HUMAN
171-207
37
1
A:171-207
37
1.10
ENST00000349736
10
ENSE00001666435
chr20:
470525-470424
102
CSK21_HUMAN
208-241
34
1
A:208-241
34
1.11b
ENST00000349736
11b
ENSE00000655089
chr20:
469422-469322
101
CSK21_HUMAN
242-275
34
1
A:242-275
34
1.12
ENST00000349736
12
ENSE00000655088
chr20:
468219-468071
149
CSK21_HUMAN
275-325
51
1
A:275-325
51
1.13
ENST00000349736
13
ENSE00000655087
chr20:
467106-467020
87
CSK21_HUMAN
325-354
30
1
A:325-329
5
1.14c
ENST00000349736
14c
ENSE00001891680
chr20:
464720-461741
2980
CSK21_HUMAN
354-391
38
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3r0ta_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Protein kinase CK2, alpha subunit
(68)
Human (Homo sapiens) [TaxId: 9606]
(36)
1a
d3r0ta_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Asym.Unit (130 KB)
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