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3ORX
Asym. Unit
Info
Asym.Unit (396 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (56 KB)
Biol.Unit 3 (56 KB)
Biol.Unit 4 (55 KB)
Biol.Unit 5 (52 KB)
Biol.Unit 6 (51 KB)
Biol.Unit 7 (52 KB)
Biol.Unit 8 (51 KB)
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(1)
Title
:
PDK1 MUTANT BOUND TO ALLOSTERIC DISULFIDE FRAGMENT INHIBITOR 1F8
Authors
:
J. D. Sadowsky, J. A. Wells
Date
:
08 Sep 10 (Deposition) - 23 Mar 11 (Release) - 27 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Pif Pocket, C-Helix, Activation Loop, Agc Kinase, Transferase, Allosteric Inhibitor, Phosphorylation, Allostery, Disulfide, Kinase, Pdk1, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. D. Sadowsky, M. A. Burlingame, D. W. Wolan, C. L. Mcclendon, M. P. Jacobson, J. A. Wells
Turning A Protein Kinase On Or Off From A Single Allosteric Site Via Disulfide Trapping.
Proc. Natl. Acad. Sci. Usa V. 108 6056 2011
[
close entry info
]
Hetero Components
(3, 19)
Info
All Hetero Components
1a: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8a)
1b: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8b)
1c: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8c)
1d: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8d)
1e: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8e)
1f: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8f)
1g: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8g)
1h: 2-METHYL-N-(2-SULFANYLETHYL)-1-BEN... (1F8h)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: PHOSPHOSERINE (SEPa)
3b: PHOSPHOSERINE (SEPb)
3c: PHOSPHOSERINE (SEPc)
3d: PHOSPHOSERINE (SEPd)
3e: PHOSPHOSERINE (SEPe)
3f: PHOSPHOSERINE (SEPf)
3g: PHOSPHOSERINE (SEPg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1F8
8
Ligand/Ion
2-METHYL-N-(2-SULFANYLETHYL)-1-BENZOFURAN-3-CARBOXAMIDE
2
CL
4
Ligand/Ion
CHLORIDE ION
3
SEP
7
Mod. Amino Acid
PHOSPHOSERINE
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:131 , CYS A:148 , PHE A:149 , GLN A:150 , LEU A:155
BINDING SITE FOR RESIDUE 1F8 A 1
02
AC2
SOFTWARE
GLU A:348 , HOH A:412
BINDING SITE FOR RESIDUE CL A 2
03
AC3
SOFTWARE
ARG B:131 , CYS B:148 , PHE B:149 , GLN B:150 , LEU B:155
BINDING SITE FOR RESIDUE 1F8 B 1
04
AC4
SOFTWARE
TRP B:347 , GLU B:348 , HOH B:1082
BINDING SITE FOR RESIDUE CL B 5
05
AC5
SOFTWARE
ARG C:131 , CYS C:148 , PHE C:149 , GLN C:150 , LEU C:155
BINDING SITE FOR RESIDUE 1F8 C 1
06
AC6
SOFTWARE
TRP C:347 , GLU C:348 , HOH C:884 , HOH C:1186
BINDING SITE FOR RESIDUE CL C 6
07
AC7
SOFTWARE
ARG D:131 , CYS D:148 , PHE D:149 , GLN D:150 , LEU D:155
BINDING SITE FOR RESIDUE 1F8 D 1
08
AC8
SOFTWARE
TRP D:347 , GLU D:348 , HOH D:1237
BINDING SITE FOR RESIDUE CL D 360
09
AC9
SOFTWARE
ARG E:131 , CYS E:148 , PHE E:149 , GLN E:150 , LEU E:155 , ILE F:119
BINDING SITE FOR RESIDUE 1F8 E 1
10
BC1
SOFTWARE
ILE E:119 , ARG F:131 , CYS F:148 , PHE F:149 , LEU F:155
BINDING SITE FOR RESIDUE 1F8 F 1
11
BC2
SOFTWARE
ARG G:131 , CYS G:148 , PHE G:149 , LEU G:155 , ILE H:119
BINDING SITE FOR RESIDUE 1F8 G 1
12
BC3
SOFTWARE
ARG H:131 , CYS H:148 , PHE H:149 , LEU H:155
BINDING SITE FOR RESIDUE 1F8 H 1
[
close Site info
]
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, 16)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:88-111,B:88-111,C:88-111,D:88-11...)
2: PROTEIN_KINASE_ST (A:201-213,B:201-213,C:201-213,D:20...)
;
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.
PDPK1_HUMAN
88-111
8
A:88-111
B:88-111
C:88-111
D:88-111
E:88-111
F:88-111
G:88-111
H:88-111
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
PDPK1_HUMAN
201-213
8
A:201-213
B:201-213
C:201-213
D:201-213
E:201-213
F:201-213
G:201-213
H:201-213
[
close PROSITE info
]
Exons
(9, 72)
Info
All Exons
Exon 1.6c (A:75-95 | B:77-95 | C:75-95 | D:76...)
Exon 1.7 (A:96-110 | B:96-110 | C:96-110 | D...)
Exon 1.8b (A:110-156 | B:110-156 | C:110-156 ...)
Exon 1.9b (A:156-204 | B:156-204 | C:156-204 ...)
Exon 1.10a (A:204-236 | B:204-236 | C:204-236 ...)
Exon 1.13 (A:238-262 | B:239-262 | C:238-262 ...)
Exon 1.14 (A:262-285 | B:262-285 | C:262-285 ...)
Exon 1.15b (A:285-317 | B:285-317 | C:285-317 ...)
Exon 1.16a (A:318-359 | B:318-359 | C:318-359 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.6c
02: Boundary 1.6c/1.7
03: Boundary 1.7/1.8b
04: Boundary 1.8b/1.9b
05: Boundary 1.9b/1.10a
06: Boundary 1.10a/1.13
07: Boundary 1.13/1.14
08: Boundary 1.14/1.15b
09: Boundary 1.15b/1.16a
10: Boundary 1.16a/1.17
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
1.1a
ENST00000342085
1a
ENSE00001944688
chr16:
2587965-2588137
173
PDPK1_HUMAN
1-8
8
0
-
-
1.6c
ENST00000342085
6c
ENSE00001640744
chr16:
2607704-2607964
261
PDPK1_HUMAN
9-95
87
8
A:75-95
B:77-95
C:75-95
D:76-95
E:76-95
F:75-95
G:75-95
H:75-95
21
19
21
20
20
21
21
21
1.7
ENST00000342085
7
ENSE00001620065
chr16:
2611481-2611523
43
PDPK1_HUMAN
96-110
15
8
A:96-110
B:96-110
C:96-110
D:96-110
E:96-110
F:96-110
G:96-110
H:96-110
15
15
15
15
15
15
15
15
1.8b
ENST00000342085
8b
ENSE00001694535
chr16:
2611772-2611909
138
PDPK1_HUMAN
110-156
47
8
A:110-156
B:110-156
C:110-156
D:110-156
E:110-156
F:110-156
G:110-156
H:110-156
47
47
47
47
47
47
47
47
1.9b
ENST00000342085
9b
ENSE00001744256
chr16:
2615554-2615698
145
PDPK1_HUMAN
156-204
49
8
A:156-204
B:156-204
C:156-204
D:156-204
E:156-204
F:156-204
G:156-204
H:156-204
49
49
49
49
49
49
49
49
1.10a
ENST00000342085
10a
ENSE00001705748
chr16:
2616357-2616454
98
PDPK1_HUMAN
204-237
34
8
A:204-236
B:204-236
C:204-236
D:204-236
E:204-231
F:204-230
G:204-230
H:204-230
33
33
33
33
28
27
27
27
1.13
ENST00000342085
13
ENSE00001704745
chr16:
2627426-2627501
76
PDPK1_HUMAN
237-262
26
8
A:238-262
B:239-262
C:238-262
D:238-262
E:242-262
F:241-262
G:241-262
H:241-262
25
24
25
25
21
22
22
22
1.14
ENST00000342085
14
ENSE00001686272
chr16:
2631296-2631364
69
PDPK1_HUMAN
262-285
24
8
A:262-285
B:262-285
C:262-285
D:262-285
E:262-285
F:262-285
G:262-285
H:262-285
24
24
24
24
24
24
24
24
1.15b
ENST00000342085
15b
ENSE00001743545
chr16:
2631608-2631704
97
PDPK1_HUMAN
285-317
33
8
A:285-317
B:285-317
C:285-317
D:285-317
E:285-317
F:285-317
G:285-317
H:285-317
33
33
33
33
33
33
33
33
1.16a
ENST00000342085
16a
ENSE00001314244
chr16:
2633413-2633586
174
PDPK1_HUMAN
318-375
58
8
A:318-359
B:318-359
C:318-359
D:318-359
E:318-359
F:318-359
G:318-359
H:318-359
42
42
42
42
42
42
42
42
1.17
ENST00000342085
17
ENSE00000946017
chr16:
2636677-2636894
218
PDPK1_HUMAN
376-448
73
0
-
-
1.18
ENST00000342085
18
ENSE00000946018
chr16:
2645794-2645851
58
PDPK1_HUMAN
448-467
20
0
-
-
1.19
ENST00000342085
19
ENSE00000946019
chr16:
2647124-2647276
153
PDPK1_HUMAN
468-518
51
0
-
-
1.20b
ENST00000342085
20b
ENSE00001505218
chr16:
2647652-2653189
5538
PDPK1_HUMAN
519-556
38
0
-
-
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3orxa_ (A:)
1b: SCOP_d3orxb_ (B:)
1c: SCOP_d3orxc_ (C:)
1d: SCOP_d3orxd_ (D:)
1e: SCOP_d3orxe_ (E:)
1f: SCOP_d3orxf_ (F:)
1g: SCOP_d3orxg_ (G:)
1h: SCOP_d3orxh_ (H:)
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(
)
(
)
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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
:
automated matches
(529)
Protein domain
:
automated matches
(529)
Human (Homo sapiens) [TaxId: 9606]
(438)
1a
d3orxa_
A:
1b
d3orxb_
B:
1c
d3orxc_
C:
1d
d3orxd_
D:
1e
d3orxe_
E:
1f
d3orxf_
F:
1g
d3orxg_
G:
1h
d3orxh_
H:
[
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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
(1, 8)
Info
all PFAM domains
1a: PFAM_Pkinase_3orxH01 (H:82-341)
1b: PFAM_Pkinase_3orxH02 (H:82-341)
1c: PFAM_Pkinase_3orxH03 (H:82-341)
1d: PFAM_Pkinase_3orxH04 (H:82-341)
1e: PFAM_Pkinase_3orxH05 (H:82-341)
1f: PFAM_Pkinase_3orxH06 (H:82-341)
1g: PFAM_Pkinase_3orxH07 (H:82-341)
1h: PFAM_Pkinase_3orxH08 (H:82-341)
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Clans
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(
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(
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Organisms
(
)
(
)
Clan
:
PKinase
(934)
Family
:
Pkinase
(680)
Homo sapiens (Human)
(521)
1a
Pkinase-3orxH01
H:82-341
1b
Pkinase-3orxH02
H:82-341
1c
Pkinase-3orxH03
H:82-341
1d
Pkinase-3orxH04
H:82-341
1e
Pkinase-3orxH05
H:82-341
1f
Pkinase-3orxH06
H:82-341
1g
Pkinase-3orxH07
H:82-341
1h
Pkinase-3orxH08
H:82-341
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