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1JWH
Asym. Unit
Info
Asym.Unit (199 KB)
Biol.Unit 1 (191 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PROTEIN KINASE CK2 HOLOENZYME
Authors
:
K. Niefind, B. Guerra, I. Ermakowa, O. G. Issinger
Date
:
04 Sep 01 (Deposition) - 04 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Casein Kinase 2, Ck2 Holoenzyme, Protein Kinase Ck2, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Niefind, B. Guerra, I. Ermakowa, O. G. Issinger
Crystal Structure Of Human Protein Kinase Ck2: Insights Into Basic Properties Of The Ck2 Holoenzyme.
Embo J. V. 20 5320 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
PO4
7
Ligand/Ion
PHOSPHATE ION
3
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:234 , ARG A:244 , HOH A:394 , HOH A:397
BINDING SITE FOR RESIDUE PO4 A 350
02
AC2
SOFTWARE
ARG B:244 , HOH B:365
BINDING SITE FOR RESIDUE PO4 B 351
03
AC3
SOFTWARE
ARG B:195 , LYS B:198 , ASN B:238 , HOH B:375
BINDING SITE FOR RESIDUE PO4 B 352
04
AC4
SOFTWARE
LYS C:147 , SER C:148 , ARG C:150 , HOH C:358 , HOH C:366
BINDING SITE FOR RESIDUE PO4 C 353
05
AC5
SOFTWARE
ARG D:17 , SER D:148 , SER D:149 , PO4 D:355 , HOH D:359 , HOH D:364
BINDING SITE FOR RESIDUE PO4 D 354
06
AC6
SOFTWARE
GLU C:57 , LYS D:147 , ARG D:150 , PO4 D:354
BINDING SITE FOR RESIDUE PO4 D 355
07
AC7
SOFTWARE
GLU D:20 , LYS D:100 , ASP D:105 , HOH D:361
BINDING SITE FOR RESIDUE PO4 D 356
08
AC8
SOFTWARE
CYS C:109 , CYS C:114 , CYS C:137 , CYS C:140 , TYR C:144
BINDING SITE FOR RESIDUE ZN C 357
09
AC9
SOFTWARE
CYS D:109 , CYS D:114 , CYS D:137 , CYS D:140 , TYR D:144
BINDING SITE FOR RESIDUE ZN D 358
10
BC1
SOFTWARE
SER A:51 , VAL A:66 , LYS A:68 , GLU A:114 , VAL A:116 , HIS A:160 , MET A:163 , ASP A:175 , HOH A:384
BINDING SITE FOR RESIDUE ANP A 340
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_077045 (R47Q, chain A/B, )
2: VAR_077046 (Y50S, chain A/B, )
3: VAR_077047 (D175G, chain A/B, )
4: VAR_077048 (K198R, chain A/B, )
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/B
R
47
Q
2
UniProt
VAR_077046
Y
50
S
CSK21_HUMAN
Disease (OCNDS)
869312849
A/B
Y
50
S
3
UniProt
VAR_077047
D
175
G
CSK21_HUMAN
Disease (OCNDS)
869312848
A/B
D
175
G
4
UniProt
VAR_077048
K
198
R
CSK21_HUMAN
Disease (OCNDS)
869312840
A/B
K
198
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:45-68,B:45-68)
2: CK2_BETA (C:109-140,D:109-140)
3: PROTEIN_KINASE_ST (A:152-164,B: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
2
A:45-68
B:45-68
2
CK2_BETA
PS01101
Casein kinase II regulatory subunit signature.
CSK2B_HUMAN
109-140
2
C:109-140
D:109-140
3
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CSK21_HUMAN
152-164
2
A:152-164
B:152-164
[
close PROSITE info
]
Exons
(17, 34)
Info
All Exons
Exon 1.3 (A:2-34 | B:2-34)
Exon 1.4 (A:34-71 | B:34-71)
Exon 1.5 (A:72-105 | B:72-105)
Exon 1.6 (A:106-122 | B:106-122)
Exon 1.7 (A:123-142 | B:123-142)
Exon 1.8 (A:143-170 | B:143-170)
Exon 1.9 (A:171-207 | B:171-207)
Exon 1.10 (A:208-241 | B:208-241)
Exon 1.11b (A:242-275 | B:242-275)
Exon 1.12 (A:275-325 | B:275-325)
Exon 1.13 (A:325-337 | B:325-336)
Exon 2.13 (C:6-24 | D:2-24)
Exon 2.15e (C:25-59 | D:25-59)
Exon 2.15j (C:59-97 | D:59-97)
Exon 2.15p (C:98-123 | D:98-123)
Exon 2.15r (C:123-186 | D:123-186)
Exon 2.15t (C:186-205 | D:186-205)
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
13: Boundary 2.12u/2.13
14: Boundary 2.13/2.15e
15: Boundary 2.15e/2.15j
16: Boundary 2.15j/2.15p
17: Boundary 2.15p/2.15r
18: Boundary 2.15r/2.15t
19: Boundary 2.15t/-
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
2
A:2-34
B:2-34
33
33
1.4
ENST00000349736
4
ENSE00001688643
chr20:
485873-485762
112
CSK21_HUMAN
34-71
38
2
A:34-71
B:34-71
38
38
1.5
ENST00000349736
5
ENSE00001705871
chr20:
480578-480477
102
CSK21_HUMAN
72-105
34
2
A:72-105
B:72-105
34
34
1.6
ENST00000349736
6
ENSE00001598088
chr20:
479949-479899
51
CSK21_HUMAN
106-122
17
2
A:106-122
B:106-122
17
17
1.7
ENST00000349736
7
ENSE00001618963
chr20:
478424-478365
60
CSK21_HUMAN
123-142
20
2
A:123-142
B:123-142
20
20
1.8
ENST00000349736
8
ENSE00000655095
chr20:
476446-476363
84
CSK21_HUMAN
143-170
28
2
A:143-170
B:143-170
28
28
1.9
ENST00000349736
9
ENSE00000655092
chr20:
473008-472898
111
CSK21_HUMAN
171-207
37
2
A:171-207
B:171-207
37
37
1.10
ENST00000349736
10
ENSE00001666435
chr20:
470525-470424
102
CSK21_HUMAN
208-241
34
2
A:208-241
B:208-241
34
34
1.11b
ENST00000349736
11b
ENSE00000655089
chr20:
469422-469322
101
CSK21_HUMAN
242-275
34
2
A:242-275
B:242-275
34
34
1.12
ENST00000349736
12
ENSE00000655088
chr20:
468219-468071
149
CSK21_HUMAN
275-325
51
2
A:275-325
B:275-325
51
51
1.13
ENST00000349736
13
ENSE00000655087
chr20:
467106-467020
87
CSK21_HUMAN
325-354
30
2
A:325-337
B:325-336
13
12
1.14c
ENST00000349736
14c
ENSE00001891680
chr20:
464720-461741
2980
CSK21_HUMAN
354-391
38
0
-
-
2.12u
ENST00000400110
12u
ENSE00001723915
HSCHR6_MHC_QBL:31624378-31624510
133
CSK2B_HUMAN
-
0
0
-
-
2.13
ENST00000400110
13
ENSE00002150158
HSCHR6_MHC_QBL:31624844-31624926
83
CSK2B_HUMAN
1-24
24
2
C:6-24
D:2-24
19
23
2.15e
ENST00000400110
15e
ENSE00001622533
HSCHR6_MHC_QBL:31625891-31625993
103
CSK2B_HUMAN
25-59
35
2
C:25-59
D:25-59
35
35
2.15j
ENST00000400110
15j
ENSE00001756289
HSCHR6_MHC_QBL:31626562-31626677
116
CSK2B_HUMAN
59-97
39
2
C:59-97
D:59-97
39
39
2.15p
ENST00000400110
15p
ENSE00002150315
HSCHR6_MHC_QBL:31627120-31627195
76
CSK2B_HUMAN
98-123
26
2
C:98-123
D:98-123
26
26
2.15r
ENST00000400110
15r
ENSE00001673157
HSCHR6_MHC_QBL:31627342-31627531
190
CSK2B_HUMAN
123-186
64
2
C:123-186
D:123-186
64
64
2.15t
ENST00000400110
15t
ENSE00001798282
HSCHR6_MHC_QBL:31627859-31628093
235
CSK2B_HUMAN
186-215
30
2
C:186-205
D:186-205
20
20
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1jwha_ (A:)
1b: SCOP_d1jwhb_ (B:)
2a: SCOP_d1jwhc_ (C:)
2b: SCOP_d1jwhd_ (D:)
View:
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Classes
(
)
(
)
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(
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(
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Superfamilies
(
)
(
)
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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
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Protein kinase CK2, alpha subunit
(68)
Human (Homo sapiens) [TaxId: 9606]
(36)
1a
d1jwha_
A:
1b
d1jwhb_
B:
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Casein kinase II beta subunit
(7)
Family
:
Casein kinase II beta subunit
(7)
Protein domain
:
Casein kinase II beta subunit
(7)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1jwhc_
C:
2b
d1jwhd_
D:
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1jwhA01 (A:25-115)
1b: CATH_1jwhB01 (B:25-115)
2a: CATH_1jwhC01 (C:6-102)
2b: CATH_1jwhD01 (D:2-102)
3a: CATH_1jwhA02 (A:7-24,A:116-333)
3b: CATH_1jwhB02 (B:7-24,B:116-333)
4a: CATH_1jwhC02 (C:103-180)
4b: CATH_1jwhD02 (D:103-180)
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Human (Homo sapiens)
(1036)
1a
1jwhA01
A:25-115
1b
1jwhB01
B:25-115
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
protein kinase ck2 holoenzyme, chain C, domain 1
(3)
Homologous Superfamily
:
protein kinase ck2 holoenzyme, chain C, domain 1
(3)
Human (Homo sapiens)
(2)
2a
1jwhC01
C:6-102
2b
1jwhD01
D:2-102
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
3a
1jwhA02
A:7-24,A:116-333
3b
1jwhB02
B:7-24,B:116-333
Class
:
Mainly Beta
(13760)
Architecture
:
Single Sheet
(341)
Topology
:
N-terminal domain of TfIIb
(166)
Homologous Superfamily
:
[code=2.20.25.20, no name defined]
(3)
Human (Homo sapiens)
(2)
4a
1jwhC02
C:103-180
4b
1jwhD02
D:103-180
[
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]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Pkinase_1jwhB01 (B:39-324)
1b: PFAM_Pkinase_1jwhB02 (B:39-324)
2a: PFAM_CK_II_beta_1jwhD01 (D:8-191)
2b: PFAM_CK_II_beta_1jwhD02 (D:8-191)
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Clans
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Organisms
(
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(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-1jwhB01
B:39-324
1b
Pkinase-1jwhB02
B:39-324
Clan
:
no clan defined [family: CK_II_beta]
(4)
Family
:
CK_II_beta
(4)
Homo sapiens (Human)
(2)
2a
CK_II_beta-1jwhD01
D:8-191
2b
CK_II_beta-1jwhD02
D:8-191
[
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