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3MKS
Asym. Unit
Info
Asym.Unit (404 KB)
Biol.Unit 1 (396 KB)
Biol.Unit 2 (202 KB)
Biol.Unit 3 (199 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YEAST CDC4/SKP1 IN COMPLEX WITH AN ALLOSTERIC INHIBITOR SCF-I2
Authors
:
S. Orlicky, F. Sicheri, M. Tyers, X. Tang
Date
:
15 Apr 10 (Deposition) - 21 Jul 10 (Release) - 21 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Keywords
:
Ubiquitin Ligase, Protein Binding, Small Molecule Complex, Ligase/Cell Cycle, Ligase-Cell Cycle Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Orlicky, X. Tang, V. Neduva, N. Elowe, E. D. Brown, F. Sicheri, M. Tyers
An Allosteric Inhibitor Of Substrate Recognition By The Scf(Cdc4) Ubiquitin Ligase.
Nat. Biotechnol. V. 28 733 2010
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: 1,1'-BINAPHTHALENE-2,2'-DICARBOXYL... (C1Ca)
2a: GLYCEROL (GOLa)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
C1C
1
Ligand/Ion
1,1'-BINAPHTHALENE-2,2'-DICARBOXYLIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
SO4
11
Ligand/Ion
SULFATE ION
[
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Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE B:280 , LYS B:311 , SER B:312 , SER B:314
BINDING SITE FOR RESIDUE SO4 B 1
02
AC2
SOFTWARE
PHE B:280
BINDING SITE FOR RESIDUE SO4 B 3
03
AC3
SOFTWARE
HOH B:29 , GLN B:389 , ARG B:639 , ASN B:720
BINDING SITE FOR RESIDUE SO4 B 4
04
AC4
SOFTWARE
HIS B:706 , ALA B:707 , ASN B:708 , ILE B:709
BINDING SITE FOR RESIDUE SO4 B 6
05
AC5
SOFTWARE
TRP B:365 , SER B:682 , ILE B:685 , PHE B:721 , GLY B:723
BINDING SITE FOR RESIDUE SO4 B 7
06
AC6
SOFTWARE
GLN D:629 , GLY D:630 , THR D:632 , ARG D:655 , GLY D:656 , TRP D:657 , ARG D:664 , PHE D:666 , SER D:667
BINDING SITE FOR RESIDUE C1C D 1
07
AC7
SOFTWARE
LYS D:665 , LEU D:699 , ARG D:700 , GLY D:702
BINDING SITE FOR RESIDUE SO4 D 2
08
AC8
SOFTWARE
ILE D:471 , VAL D:472 , GLU D:473 , HIS D:539 , GLY D:540
BINDING SITE FOR RESIDUE SO4 D 5
09
AC9
SOFTWARE
ARG D:467 , ARG D:485 , TYR D:548
BINDING SITE FOR RESIDUE SO4 D 8
10
BC1
SOFTWARE
GLN D:340 , HIS D:432
BINDING SITE FOR RESIDUE SO4 D 9
11
BC2
SOFTWARE
PRO D:279 , PHE D:280
BINDING SITE FOR RESIDUE SO4 D 10
12
BC3
SOFTWARE
LEU D:284 , LYS D:311 , SER D:312 , THR D:313 , SER D:314
BINDING SITE FOR RESIDUE SO4 D 11
13
BC4
SOFTWARE
HOH D:38 , GLN D:389 , ARG D:639 , TYR D:680 , ASN D:720
BINDING SITE FOR RESIDUE GOL D 745
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 10)
Info
All PROSITE Patterns/Profiles
1: FBOX (B:272-319,D:272-319)
2: WD_REPEATS_1 (B:436-450,D:436-450|B:543-557,D:54...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FBOX
PS50181
F-box domain profile.
CDC4_YEAST
272-319
2
B:272-319
D:272-319
2
WD_REPEATS_1
PS00678
Trp-Asp (WD) repeats signature.
CDC4_YEAST
436-450
543-557
585-599
645-659
8
B:436-450
D:436-450
B:543-557
D:543-557
B:585-599
D:585-599
B:645-659
D:645-659
[
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Exons
(2, 4)
Info
All Exons
Exon 1.1 (A:4-185 (gaps) | C:4-186 (gaps))
Exon 2.1 (B:270-744 (gaps) | D:269-744 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
3: Boundary -/2.1
4: Boundary 2.1/-
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
YDR328C
1
YDR328C.1
IV:1126014-1125430
585
SKP1_YEAST
1-194
194
2
A:4-185 (gaps)
C:4-186 (gaps)
182
183
2.1
YFL009W
1
YFL009W.1
VI:116139-118478
2340
CDC4_YEAST
1-779
779
2
B:270-744 (gaps)
D:269-744 (gaps)
475
476
[
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SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3mksb1 (B:270-369)
1b: SCOP_d3mksd1 (D:269-369)
2a: SCOP_d3mksa2 (A:116-185)
2b: SCOP_d3mksc2 (C:116-186)
3a: SCOP_d3mksb2 (B:370-744)
3b: SCOP_d3mksd2 (D:370-744)
4a: SCOP_d3mksa1 (A:4-103)
4b: SCOP_d3mksc1 (C:4-103)
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(
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
F-box domain
(12)
Superfamily
:
F-box domain
(12)
Family
:
F-box domain
(12)
Protein domain
:
Cdc4 F-box and linker domains
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d3mksb1
B:270-369
1b
d3mksd1
D:269-369
Fold
:
Skp1 dimerisation domain-like
(18)
Superfamily
:
Skp1 dimerisation domain-like
(18)
Family
:
Skp1 dimerisation domain-like
(13)
Protein domain
:
Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
2a
d3mksa2
A:116-185
2b
d3mksc2
C:116-186
Class
:
All beta proteins
(24004)
Fold
:
7-bladed beta-propeller
(245)
Superfamily
:
WD40 repeat-like
(95)
Family
:
WD40-repeat
(53)
Protein domain
:
Cdc4 propeller domain
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
3a
d3mksb2
B:370-744
3b
d3mksd2
D:370-744
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
POZ domain
(79)
Superfamily
:
POZ domain
(79)
Family
:
BTB/POZ domain
(43)
Protein domain
:
Centromere DNA-binding protein complex Cbf3 subunit D, CBF3D
(2)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
4a
d3mksa1
A:4-103
4b
d3mksc1
C:4-103
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(4, 18)
Info
all PFAM domains
1a: PFAM_WD40_3mksD01 (D:625-658)
1b: PFAM_WD40_3mksD02 (D:625-658)
1c: PFAM_WD40_3mksD03 (D:625-658)
1d: PFAM_WD40_3mksD04 (D:625-658)
1e: PFAM_WD40_3mksD05 (D:625-658)
1f: PFAM_WD40_3mksD06 (D:625-658)
1g: PFAM_WD40_3mksD07 (D:625-658)
1h: PFAM_WD40_3mksD08 (D:625-658)
1i: PFAM_WD40_3mksD09 (D:625-658)
1j: PFAM_WD40_3mksD10 (D:625-658)
1k: PFAM_WD40_3mksD11 (D:625-658)
1l: PFAM_WD40_3mksD12 (D:625-658)
2a: PFAM_F_box_3mksD13 (D:273-320)
2b: PFAM_F_box_3mksD14 (D:273-320)
3a: PFAM_Skp1_POZ_3mksC01 (C:75-99)
3b: PFAM_Skp1_POZ_3mksC02 (C:75-99)
4a: PFAM_Skp1_3mksC03 (C:116-186)
4b: PFAM_Skp1_3mksC04 (C:116-186)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
WD40
(64)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(18)
1a
WD40-3mksD01
D:625-658
1b
WD40-3mksD02
D:625-658
1c
WD40-3mksD03
D:625-658
1d
WD40-3mksD04
D:625-658
1e
WD40-3mksD05
D:625-658
1f
WD40-3mksD06
D:625-658
1g
WD40-3mksD07
D:625-658
1h
WD40-3mksD08
D:625-658
1i
WD40-3mksD09
D:625-658
1j
WD40-3mksD10
D:625-658
1k
WD40-3mksD11
D:625-658
1l
WD40-3mksD12
D:625-658
Clan
:
F-box
(7)
Family
:
F-box
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
2a
F-box-3mksD13
D:273-320
2b
F-box-3mksD14
D:273-320
Clan
:
POZ
(36)
Family
:
Skp1_POZ
(18)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
3a
Skp1_POZ-3mksC01
C:75-99
3b
Skp1_POZ-3mksC02
C:75-99
Clan
:
no clan defined [family: Skp1]
(15)
Family
:
Skp1
(15)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
4a
Skp1-3mksC03
C:116-186
4b
Skp1-3mksC04
C:116-186
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