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2AST
Asym. Unit
Info
Asym.Unit (102 KB)
Biol.Unit 1 (96 KB)
Biol.Unit 2 (189 KB)
Biol.Unit 3 (189 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SKP1-SKP2-CKS1 IN COMPLEX WITH A P27 PEPTIDE
Authors
:
B. Hao, N. Zhang, B. A. Schulman, G. Wu, M. Pagano, N. P. Pavletich
Date
:
24 Aug 05 (Deposition) - 18 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B,C,D (2x)
Biol. Unit 3: A,B,C,D (2x)
Keywords
:
Scf-Substrate Complex, Lrr, Cell Cycle, Protein Turnover Complex, Ligase-Ligase Inhibitor Complex
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Hao, N. Zheng, B. A. Schulman, G. Wu, J. J. Miller, M. Pagano, N. P. Pavletich
Structural Basis Of The Cks1-Dependent Recognition Of P27(Kip1) By The Scf(Skp2) Ubiquitin Ligase.
Mol. Cell V. 20 9 2005
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: BENZAMIDINE (BENa)
1b: BENZAMIDINE (BENb)
2a: PHOSPHOTHREONINE (TPOa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEN
2
Ligand/Ion
BENZAMIDINE
2
TPO
1
Mod. Amino Acid
PHOSPHOTHREONINE
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE B:2169 , VAL B:2192 , HOH C:100 , HOH C:182 , HOH C:247 , MET C:3058 , ARG C:3070
BINDING SITE FOR RESIDUE BEN C 1001
2
AC2
SOFTWARE
HOH B:67 , HOH B:74 , HOH B:263 , ALA B:2227 , SER B:2230 , SER B:2254 , HIS C:3021 , HIS C:3060 , GLU C:3063 , ILE C:3066
BINDING SITE FOR RESIDUE BEN B 1002
3
AC3
SOFTWARE
HOH B:13 , ARG B:2294 , TYR B:2346 , ASP B:2347 , TYR C:3008 , ASP C:3010 , LYS C:3011 , ARG C:3020 , ARG C:3044 , GLN C:3049 , GLN C:3050 , SER C:3051 , GLN C:3052 , TRP C:3054
BINDING SITE FOR CHAIN D OF CYCLIN-DEPENDENT KINASE INHIBITOR 1B
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_051999 (F1014L, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_051999
F
14
L
SKP1_HUMAN
Polymorphism
11538034
A
F
1014
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: CKS_1 (C:3008-3026)
2: CKS_2 (C:3060-3070)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CKS_1
PS00944
Cyclin-dependent kinases regulatory subunits signature 1.
CKS1_HUMAN
8-26
1
C:3008-3026
2
CKS_2
PS00945
Cyclin-dependent kinases regulatory subunits signature 2.
CKS1_HUMAN
60-70
1
C:3060-3070
[
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Exons
(17, 17)
Info
All Exons
Exon 1.4 (D:4181-4190)
Exon 2.3 (B:2095-2131)
Exon 2.4 (B:2131-2179)
Exon 2.5 (B:2179-2224)
Exon 2.6b (B:2224-2257)
Exon 2.7 (B:2257-2301)
Exon 2.8 (B:2301-2318)
Exon 2.9 (B:2318-2354)
Exon 2.12c (B:2354-2419)
Exon 3.1c (C:3005-3020)
Exon 3.4b (C:3020-3063)
Exon 3.5f (C:3063-3073)
Exon 4.5b (A:1002-1033)
Exon 4.7 (A:1033-1051 (gaps))
Exon 4.8d (A:1052-1105 (gaps))
Exon 4.9d (A:1106-1152)
Exon 4.9l (A:1153-1160)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3a/1.4
02: Boundary 1.4/1.5c
03: Boundary 2.2a/2.3
04: Boundary 2.3/2.4
05: Boundary 2.4/2.5
06: Boundary 2.5/2.6b
07: Boundary 2.6b/2.7
08: Boundary 2.7/2.8
09: Boundary 2.8/2.9
10: Boundary 2.9/2.12c
11: Boundary 2.12c/-
12: Boundary -/3.1c
13: Boundary 3.1c/3.4b
14: Boundary 3.4b/3.5f
15: Boundary 3.5f/-
16: Boundary 4.2a/4.5b
17: Boundary 4.5b/4.7
18: Boundary 4.7/4.8d
19: Boundary 4.8d/4.9d
20: Boundary 4.9d/4.9l
21: Boundary 4.9l/-
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
1.3a
ENST00000228872
3a
ENSE00000721808
chr12:
12870397-12871248
852
CDN1B_HUMAN
1-159
159
0
-
-
1.4
ENST00000228872
4
ENSE00000822053
chr12:
12871759-12871888
130
CDN1B_HUMAN
159-198
40
1
D:4181-4190
10
1.5c
ENST00000228872
5c
ENSE00000993687
chr12:
12873970-12875305
1336
CDN1B_HUMAN
-
0
0
-
-
2.1b
ENST00000274255
1b
ENSE00001852758
chr5:
36152169-36152372
204
SKP2_HUMAN
1-3
3
0
-
-
2.2a
ENST00000274255
2a
ENSE00001130153
chr5:
36152873-36153144
272
SKP2_HUMAN
3-94
92
0
-
-
2.3
ENST00000274255
3
ENSE00001006180
chr5:
36163747-36163858
112
SKP2_HUMAN
94-131
38
1
B:2095-2131
37
2.4
ENST00000274255
4
ENSE00001006177
chr5:
36166621-36166764
144
SKP2_HUMAN
131-179
49
1
B:2131-2179
49
2.5
ENST00000274255
5
ENSE00001006179
chr5:
36168415-36168549
135
SKP2_HUMAN
179-224
46
1
B:2179-2224
46
2.6b
ENST00000274255
6b
ENSE00001006176
chr5:
36170446-36170544
99
SKP2_HUMAN
224-257
34
1
B:2224-2257
34
2.7
ENST00000274255
7
ENSE00002147593
chr5:
36171705-36171835
131
SKP2_HUMAN
257-301
45
1
B:2257-2301
45
2.8
ENST00000274255
8
ENSE00000971194
chr5:
36177067-36177118
52
SKP2_HUMAN
301-318
18
1
B:2301-2318
18
2.9
ENST00000274255
9
ENSE00000971195
chr5:
36177287-36177394
108
SKP2_HUMAN
318-354
37
1
B:2318-2354
37
2.12c
ENST00000274255
12c
ENSE00001082238
chr5:
36181920-36184421
2502
SKP2_HUMAN
354-424
71
1
B:2354-2419
66
3.1c
ENST00000308987
1c
ENSE00001200321
chr1:
154947175-154947280
106
CKS1_HUMAN
1-20
20
1
C:3005-3020
16
3.4b
ENST00000308987
4b
ENSE00001200312
chr1:
154950463-154950590
128
CKS1_HUMAN
20-63
44
1
C:3020-3063
44
3.5f
ENST00000308987
5f
ENSE00001848352
chr1:
154951201-154951725
525
CKS1_HUMAN
63-79
17
1
C:3063-3073
11
4.2a
ENST00000353411
2a
ENSE00001169035
chr5:
133512729-133512546
184
SKP1_HUMAN
-
0
0
-
-
4.5b
ENST00000353411
5b
ENSE00000763313
chr5:
133509713-133509617
97
SKP1_HUMAN
1-33
33
1
A:1002-1033
32
4.7
ENST00000353411
7
ENSE00002156080
chr5:
133502934-133502861
74
SKP1_HUMAN
33-57
25
1
A:1033-1051 (gaps)
25
4.8d
ENST00000353411
8d
ENSE00000763311
chr5:
133496821-133496678
144
SKP1_HUMAN
58-105
48
1
A:1052-1105 (gaps)
54
4.9d
ENST00000353411
9d
ENSE00001328116
chr5:
133494286-133494146
141
SKP1_HUMAN
106-152
47
1
A:1106-1152
47
4.9l
ENST00000353411
9l
ENSE00001291683
chr5:
133493459-133492082
1378
SKP1_HUMAN
153-163
11
1
A:1153-1160
8
[
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SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2astb1 (B:2097-2135)
2a: SCOP_d2astc_ (C:)
3a: SCOP_d2astb2 (B:2136-2419)
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Protein Domains
(
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
F-box domain
(12)
Superfamily
:
F-box domain
(12)
Family
:
F-box domain
(12)
Protein domain
:
Skp2
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d2astb1
B:2097-2135
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cell cycle regulatory proteins
(11)
Superfamily
:
Cell cycle regulatory proteins
(11)
Family
:
Cell cycle regulatory proteins
(11)
Protein domain
:
CksHs1
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d2astc_
C:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
RNI-like
(17)
Family
:
Cyclin A/CDK2-associated p19, Skp2
(4)
Protein domain
:
Cyclin A/CDK2-associated p19, Skp2
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
3a
d2astb2
B:2136-2419
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2astC00 (C:3005-3073)
2a: CATH_2astA00 (A:1002-1160)
3a: CATH_2astB00 (B:2095-2419)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Cyclin-Dependent Kinase Subunit Type 2
(9)
Homologous Superfamily
:
Cyclin-Dependent Kinase Subunit Type 2
(9)
Human (Homo sapiens)
(6)
1a
2astC00
C:3005-3073
Topology
:
Potassium Channel Kv1.1; Chain A
(53)
Homologous Superfamily
:
Potassium Channel Kv1.1; Chain A
(53)
Human (Homo sapiens)
(30)
2a
2astA00
A:1002-1160
Architecture
:
Alpha-Beta Horseshoe
(92)
Topology
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(73)
Homologous Superfamily
:
Ribonuclease Inhibitor
(73)
Human (Homo sapiens)
(26)
3a
2astB00
B:2095-2419
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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