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2CCH
Asym. Unit
Info
Asym.Unit (427 KB)
Biol.Unit 1 (223 KB)
Biol.Unit 2 (198 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF CDK2 CYCLIN A IN COMPLEX WITH A SUBSTRATE PEPTIDE DERIVED FROM CDC MODIFIED WITH A GAMMA-LINKED ATP ANALOGUE
Authors
:
K. Y. Cheng, M. E. M. Noble, V. Skamnaki, N. R. Brown, E. D. Lowe, L. Kontogiannis, K. Shen, P. A. Cole, G. Siligardi, L. N. Johnson
Date
:
16 Jan 06 (Deposition) - 03 May 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,E (1x)
Biol. Unit 2: C,D,F (1x)
Keywords
:
Complex(Transferase/Cell Division), Atp-Binding, Cdk2, Cell Cycle, Cell Division, Cyclin, Mitosis, Nuclear Protein, Peptide Specificity, Phosphorylation, Polymorphism, Protein Kinase, Recruitment, Serine-Threonine-Protein Kinase, Serine/Threonine-Protein Kinase, Transferase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Y. Cheng, M. E. M. Noble, V. Skamnaki, N. R. Brown, E. D. Lowe, L. Kontogiannis, K. Shen, P. A. Cole, G. Siligardi, L. N. Johnson
The Role Of The Phospho-Cdk2/Cyclin A Recruitment Site In Substrate Recognition
J. Biol. Chem. V. 281 23167 2006
[
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Hetero Components
(4, 7)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: SULFATE ION (SO4a)
4a: PHOSPHOTHREONINE (TPOa)
4b: PHOSPHOTHREONINE (TPOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
SO4
1
Ligand/Ion
SULFATE ION
4
TPO
2
Mod. Amino Acid
PHOSPHOTHREONINE
[
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:214 , ARG A:217 , LYS A:278 , HOH A:2383 , HOH A:2384 , HOH A:2385 , HOH A:2386 , HOH B:2070
BINDING SITE FOR RESIDUE SO4 A1298
2
AC2
SOFTWARE
ILE A:10 , GLY A:11 , GLU A:12 , TYR A:15 , VAL A:18 , ALA A:31 , LYS A:33 , GLU A:81 , PHE A:82 , LEU A:83 , ASP A:86 , LYS A:89 , LYS A:129 , GLN A:131 , ASN A:132 , LEU A:134 , ASP A:145 , GLY A:147 , LEU A:148 , HOH A:2037 , HOH A:2374 , HOH A:2375 , HOH A:2376 , HOH A:2377 , HOH A:2378 , HOH A:2379 , HOH A:2380 , HOH A:2381
BINDING SITE FOR RESIDUE ATP A1297
3
AC3
SOFTWARE
ILE C:10 , GLY C:11 , GLU C:12 , TYR C:15 , ALA C:31 , LYS C:33 , GLU C:81 , PHE C:82 , LEU C:83 , ASP C:86 , LYS C:89 , LYS C:129 , GLN C:131 , ASN C:132 , LEU C:134 , ASP C:145 , GLY C:147 , LEU C:148 , HOH C:2089 , HOH C:2141 , HOH C:2142 , HOH C:2143 , HOH C:2144
BINDING SITE FOR RESIDUE ATP C1297
4
AC4
SOFTWARE
PHE A:109 , ILE A:209 , PHE A:213 , LYS A:237 , SER A:239 , PHE A:286 , GLN A:287 , HOH A:2387 , HOH A:2388
BINDING SITE FOR RESIDUE GOL A1299
5
AC5
SOFTWARE
HIS A:60 , GLN A:113 , ALA A:116 , PHE A:117 , LYS A:242 , TRP A:243 , HOH A:2285 , HOH A:2389 , HOH A:2390
BINDING SITE FOR RESIDUE GOL A1300
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016157 (Y15S, chain A/C, )
2: VAR_053927 (V18L, chain A/C, )
3: VAR_041972 (P45L, chain A/C, )
4: VAR_019988 (T290S, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016157
Y
15
S
CDK2_HUMAN
Polymorphism
3087335
A/C
Y
15
S
2
UniProt
VAR_053927
V
18
L
CDK2_HUMAN
Polymorphism
11554376
A/C
V
18
L
3
UniProt
VAR_041972
P
45
L
CDK2_HUMAN
Unclassified
---
A/C
P
45
L
4
UniProt
VAR_019988
T
290
S
CDK2_HUMAN
Polymorphism
2069413
A/C
T
290
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:10-33,C:10-33)
2: PROTEIN_KINASE_ST (A:123-135,C:123-135)
3: CYCLINS (B:211-242,D:211-242)
;
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.
CDK2_HUMAN
10-33
2
A:10-33
C:10-33
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CDK2_HUMAN
123-135
2
A:123-135
C:123-135
3
CYCLINS
PS00292
Cyclins signature.
CCNA2_HUMAN
211-242
2
B:211-242
D:211-242
[
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Exons
(14, 28)
Info
All Exons
Exon 1.3b (E:1-12 | F:1-12)
Exon 2.1 (A:1-39 | C:1-39)
Exon 2.2 (A:39-65 | C:39-65)
Exon 2.3 (A:65-105 | C:65-105)
Exon 2.4 (A:106-162 | C:106-162)
Exon 2.5 (A:163-196 | C:163-196)
Exon 2.6 (A:197-264 | C:197-264)
Exon 2.7 (A:265-296 | C:265-296)
Exon 3.3 (B:173-190 | D:176-190)
Exon 3.4 (B:191-265 | D:191-265)
Exon 3.5 (B:265-334 | D:265-334)
Exon 3.6 (B:335-372 | D:335-372)
Exon 3.7 (B:373-417 | D:373-417)
Exon 3.8 (B:417-432 | D:417-431)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2b/1.3b
02: Boundary 1.3b/1.4
03: Boundary -/2.1
04: Boundary 2.1/2.2
05: Boundary 2.2/2.3
06: Boundary 2.3/2.4
07: Boundary 2.4/2.5
08: Boundary 2.5/2.6
09: Boundary 2.6/2.7
10: Boundary 2.7/-
11: Boundary 3.2/3.3
12: Boundary 3.3/3.4
13: Boundary 3.4/3.5
14: Boundary 3.5/3.6
15: Boundary 3.6/3.7
16: Boundary 3.7/3.8
17: Boundary 3.8/-
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
1.1
ENST00000209728
1
ENSE00001297162
chr17:
38443885-38444342
458
CDC6_HUMAN
-
0
0
-
-
1.2b
ENST00000209728
2b
ENSE00001118352
chr17:
38445660-38445850
191
CDC6_HUMAN
1-60
60
0
-
-
1.3b
ENST00000209728
3b
ENSE00001118359
chr17:
38447310-38447591
282
CDC6_HUMAN
60-154
95
2
E:1-12
F:1-12
12
12
1.4
ENST00000209728
4
ENSE00001118354
chr17:
38447721-38447920
200
CDC6_HUMAN
154-220
67
0
-
-
1.5
ENST00000209728
5
ENSE00001118356
chr17:
38449708-38449883
176
CDC6_HUMAN
221-279
59
0
-
-
1.6
ENST00000209728
6
ENSE00001118353
chr17:
38450202-38450308
107
CDC6_HUMAN
279-315
37
0
-
-
1.7
ENST00000209728
7
ENSE00001118357
chr17:
38450616-38450755
140
CDC6_HUMAN
315-361
47
0
-
-
1.8
ENST00000209728
8
ENSE00001118358
chr17:
38451608-38451708
101
CDC6_HUMAN
362-395
34
0
-
-
1.9
ENST00000209728
9
ENSE00001118360
chr17:
38452955-38453019
65
CDC6_HUMAN
395-417
23
0
-
-
1.10
ENST00000209728
10
ENSE00001058106
chr17:
38457080-38457282
203
CDC6_HUMAN
417-484
68
0
-
-
1.11
ENST00000209728
11
ENSE00000720428
chr17:
38457720-38457860
141
CDC6_HUMAN
485-531
47
0
-
-
1.12
ENST00000209728
12
ENSE00001182286
chr17:
38458164-38459171
1008
CDC6_HUMAN
532-560
29
0
-
-
2.1
ENST00000266970
1
ENSE00001301614
chr12:
56360556-56360908
353
CDK2_HUMAN
1-39
39
2
A:1-39
C:1-39
39
39
2.2
ENST00000266970
2
ENSE00000838625
chr12:
56361641-56361718
78
CDK2_HUMAN
39-65
27
2
A:39-65
C:39-65
27
27
2.3
ENST00000266970
3
ENSE00000838626
chr12:
56361833-56361953
121
CDK2_HUMAN
65-105
41
2
A:65-105
C:65-105
41
41
2.4
ENST00000266970
4
ENSE00000838629
chr12:
56362562-56362732
171
CDK2_HUMAN
106-162
57
2
A:106-162
C:106-162
57
57
2.5
ENST00000266970
5
ENSE00001704611
chr12:
56363259-56363360
102
CDK2_HUMAN
163-196
34
2
A:163-196
C:163-196
34
34
2.6
ENST00000266970
6
ENSE00000938649
chr12:
56364828-56365031
204
CDK2_HUMAN
197-264
68
2
A:197-264
C:197-264
68
68
2.7
ENST00000266970
7
ENSE00001215687
chr12:
56365305-56366565
1261
CDK2_HUMAN
265-298
34
2
A:265-296
C:265-296
32
32
3.1
ENST00000274026
1
ENSE00001176937
chr4:
122745087-122744571
517
CCNA2_HUMAN
1-71
71
0
-
-
3.2
ENST00000274026
2
ENSE00000970332
chr4:
122743801-122743558
244
CCNA2_HUMAN
72-153
82
0
-
-
3.3
ENST00000274026
3
ENSE00000970333
chr4:
122742246-122742134
113
CCNA2_HUMAN
153-190
38
2
B:173-190
D:176-190
18
15
3.4
ENST00000274026
4
ENSE00000970329
chr4:
122741920-122741697
224
CCNA2_HUMAN
191-265
75
2
B:191-265
D:191-265
75
75
3.5
ENST00000274026
5
ENSE00000970330
chr4:
122740734-122740527
208
CCNA2_HUMAN
265-334
70
2
B:265-334
D:265-334
70
70
3.6
ENST00000274026
6
ENSE00001016934
chr4:
122740068-122739955
114
CCNA2_HUMAN
335-372
38
2
B:335-372
D:335-372
38
38
3.7
ENST00000274026
7
ENSE00001016935
chr4:
122739332-122739199
134
CCNA2_HUMAN
373-417
45
2
B:373-417
D:373-417
45
45
3.8
ENST00000274026
8
ENSE00001176933
chr4:
122738841-122737599
1243
CCNA2_HUMAN
417-432
16
2
B:417-432
D:417-431
16
15
[
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SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d2cchb1 (B:181-308)
1b: SCOP_d2cchb2 (B:309-432)
1c: SCOP_d2cchd1 (D:181-308)
1d: SCOP_d2cchd2 (D:309-431)
2a: SCOP_d2ccha_ (A:)
2b: SCOP_d2cchc_ (C:)
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Protein Domains
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(
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Organisms
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cyclin-like
(137)
Superfamily
:
Cyclin-like
(137)
Family
:
Cyclin
(117)
Protein domain
:
Cyclin A
(82)
Human (Homo sapiens) [TaxId: 9606]
(73)
1a
d2cchb1
B:181-308
1b
d2cchb2
B:309-432
1c
d2cchd1
D:181-308
1d
d2cchd2
D:309-431
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
:
Cyclin-dependent PK, CDK2
(340)
Human (Homo sapiens) [TaxId: 9606]
(336)
2a
d2ccha_
A:
2b
d2cchc_
C:
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_2cchA01 (A:0-84)
1b: CATH_2cchC01 (C:0-84)
2a: CATH_2cchD01 (D:181-194,D:308-431)
2b: CATH_2cchB01 (B:181-194,B:308-432)
2c: CATH_2cchB02 (B:195-307)
2d: CATH_2cchD02 (D:195-307)
3a: CATH_2cchA02 (A:85-295)
3b: CATH_2cchC02 (C:85-295)
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Topologies
(
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(
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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
2cchA01
A:0-84
1b
2cchC01
C:0-84
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cyclin A; domain 1
(136)
Homologous Superfamily
:
[code=1.10.472.10, no name defined]
(99)
Human (Homo sapiens)
(84)
2a
2cchD01
D:181-194,D:308-431
2b
2cchB01
B:181-194,B:308-432
2c
2cchB02
B:195-307
2d
2cchD02
D:195-307
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
3a
2cchA02
A:85-295
3b
2cchC02
C:85-295
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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