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2IVU
Asym. Unit
Info
Asym.Unit (53 KB)
Biol.Unit 1 (93 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN COMPLEXED WITH THE INHIBITOR ZD6474
Authors
:
P. P. Knowles, J. Murray-Rust, N. Q. Mcdonald
Date
:
16 Jun 06 (Deposition) - 10 Aug 06 (Release) - 28 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Nucleotide-Binding, Hirschsprung Disease, Phosphorylation, Disease Mutation, Phosphotransferase, Tyrosine-Protein Kinase, Chromosomal Translocation, Polymorphism, Gdnf Receptor, Transmembrane, Proto- Oncogene, Tyrosine Kinase, Ret, Kinase, Membrane, Atp-Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. P. Knowles, J. Murray-Rust, S. Kjaer, R. P. Scott, S. Hanrahan, M. Santoro, C. F. Ibanez, N. Q. Mcdonald
Structure And Chemical Inhibition Of The Ret Tyrosine Kinas Domain.
J. Biol. Chem. V. 281 33577 2006
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
1b: FORMIC ACID (FMTb)
2a: O-PHOSPHOTYROSINE (PTRa)
3a: 4-BROMO-2-FLUORO-N-[(4E)-6-METHOXY... (ZD6a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
2
Ligand/Ion
FORMIC ACID
2
PTR
1
Mod. Amino Acid
O-PHOSPHOTYROSINE
3
ZD6
1
Ligand/Ion
4-BROMO-2-FLUORO-N-[(4E)-6-METHOXY-7-[(1-METHYLPIPERIDIN-4-YL)METHOXY]QUINAZOLIN-4(1H)-YLIDENE]ANILINE
[
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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
LEU A:730 , VAL A:738 , ALA A:756 , LYS A:758 , GLU A:775 , LEU A:779 , VAL A:804 , GLU A:805 , TYR A:806 , ALA A:807 , LYS A:808 , GLY A:810 , LEU A:881 , SER A:891 , HOH A:2071
BINDING SITE FOR RESIDUE ZD6 A3015
2
AC2
SOFTWARE
GLY A:700 , PRO A:701 , LEU A:702 , SER A:703 , GLN A:910 , LEU A:923 , PHE A:924 , HIS A:926
BINDING SITE FOR RESIDUE FMT A3013
3
AC3
SOFTWARE
ARG A:873 , LYS A:907 , GLY A:911 , ARG A:912
BINDING SITE FOR RESIDUE FMT A3014
[
close Site info
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SAPs(SNPs)/Variants
(31, 31)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_041765 (R749T, chain A, )
02: VAR_009481 (E762Q, chain A, )
03: VAR_009493 (S765P, chain A, )
04: VAR_006334 (S767R, chain A, )
05: VAR_006335 (E768D, chain A, )
06: VAR_044395 (V778I, chain A, )
07: VAR_067119 (N783S, chain A, )
08: VAR_009482 (L790F, chain A, )
09: VAR_009483 (Y791F, chain A, )
10: VAR_006336 (V804L, chain A, )
11: VAR_006337 (V804M, chain A, )
12: VAR_009484 (R813Q, chain A, )
13: VAR_011582 (R844L, chain A, )
14: VAR_006338 (R873Q, chain A, )
15: VAR_009485 (A883F, chain A, )
16: VAR_009486 (S891A, chain A, )
17: VAR_006339 (F893L, chain A, )
18: VAR_044396 (G894S, chain A, )
19: VAR_006340 (R897Q, chain A, )
20: VAR_006341 (K907E, chain A, )
21: VAR_067121 (K907T, chain A, )
22: VAR_006342 (M918T, chain A, )
23: VAR_006343 (E921K, chain A, )
24: VAR_012745 (S922F, chain A, )
25: VAR_009487 (S922Y, chain A, )
26: VAR_006345 (T946M, chain A, )
27: VAR_067122 (F961L, chain A, )
28: VAR_006346 (R972G, chain A, )
29: VAR_006347 (P973L, chain A, )
30: VAR_006348 (M980T, chain A, )
31: VAR_006349 (R982C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_041765
R
749
T
RET_HUMAN
Polymorphism
34288963
A
R
749
T
02
UniProt
VAR_009481
E
762
Q
RET_HUMAN
Disease (HSCR1)
---
A
E
762
Q
03
UniProt
VAR_009493
S
765
P
RET_HUMAN
Disease (HSCR1)
75075748
A
S
765
P
04
UniProt
VAR_006334
S
767
R
RET_HUMAN
Disease (HSCR1)
---
A
S
767
R
05
UniProt
VAR_006335
E
768
D
RET_HUMAN
Disease (MTC)
78014899
A
E
768
D
06
UniProt
VAR_044395
V
778
I
RET_HUMAN
Unclassified
75686697
A
V
778
I
07
UniProt
VAR_067119
N
783
S
RET_HUMAN
Disease (HSCR1)
---
A
N
783
S
08
UniProt
VAR_009482
L
790
F
RET_HUMAN
Disease (MEN2A)
75030001
A
L
790
F
09
UniProt
VAR_009483
Y
791
F
RET_HUMAN
Disease (PCC)
77724903
A
Y
791
F
10
UniProt
VAR_006336
V
804
L
RET_HUMAN
Disease (MTC)
79658334
A
V
804
L
11
UniProt
VAR_006337
V
804
M
RET_HUMAN
Disease (MTC)
79658334
A
V
804
M
12
UniProt
VAR_009484
R
813
Q
RET_HUMAN
Disease (HSCR1)
---
A
R
813
Q
13
UniProt
VAR_011582
R
844
L
RET_HUMAN
Disease (MTC)
55947360
A
R
844
L
14
UniProt
VAR_006338
R
873
Q
RET_HUMAN
Disease (HSCR1)
---
A
R
873
Q
15
UniProt
VAR_009485
A
883
F
RET_HUMAN
Disease (MEN2B)
---
A
A
883
F
16
UniProt
VAR_009486
S
891
A
RET_HUMAN
Disease (MTC)
75234356
A
S
891
A
17
UniProt
VAR_006339
F
893
L
RET_HUMAN
Disease (HSCR1)
---
A
F
893
L
18
UniProt
VAR_044396
G
894
S
RET_HUMAN
Unclassified
---
A
G
894
S
19
UniProt
VAR_006340
R
897
Q
RET_HUMAN
Disease (HSCR1)
76087194
A
R
897
Q
20
UniProt
VAR_006341
K
907
E
RET_HUMAN
Disease (HSCR1)
---
A
K
907
E
21
UniProt
VAR_067121
K
907
T
RET_HUMAN
Disease (HSCR1)
---
A
K
907
T
22
UniProt
VAR_006342
M
918
T
RET_HUMAN
Disease (MEN2B)
74799832
A
M
918
T
23
UniProt
VAR_006343
E
921
K
RET_HUMAN
Disease (HSCR1)
---
A
E
921
K
24
UniProt
VAR_012745
S
922
F
RET_HUMAN
Disease (MTC)
---
A
S
922
F
25
UniProt
VAR_009487
S
922
Y
RET_HUMAN
Polymorphism
---
A
S
922
Y
26
UniProt
VAR_006345
T
946
M
RET_HUMAN
Disease (MEN2B)
---
A
T
946
M
27
UniProt
VAR_067122
F
961
L
RET_HUMAN
Disease (HSCR1)
---
A
F
961
L
28
UniProt
VAR_006346
R
972
G
RET_HUMAN
Disease (HSCR1)
76534745
A
R
972
G
29
UniProt
VAR_006347
P
973
L
RET_HUMAN
Disease (HSCR1)
---
A
P
973
L
30
UniProt
VAR_006348
M
980
T
RET_HUMAN
Disease (HSCR1)
---
A
M
980
T
31
UniProt
VAR_006349
R
982
C
RET_HUMAN
Polymorphism
17158558
A
R
982
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:730-758)
2: PROTEIN_KINASE_TYR (A:870-882)
;
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.
RET_HUMAN
730-758
1
A:730-758
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
RET_HUMAN
870-882
1
A:870-882
[
close PROSITE info
]
Exons
(8, 8)
Info
All Exons
Exon 1.11b (A:700-712 (gaps))
Exon 1.12 (A:714-762)
Exon 1.13 (A:762-798)
Exon 1.14 (A:798-869 (gaps))
Exon 1.15 (A:870-910)
Exon 1.16 (A:911-934)
Exon 1.17 (A:934-980)
Exon 1.18 (A:980-1012)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11b
2: Boundary 1.11b/1.12
3: Boundary 1.12/1.13
4: Boundary 1.13/1.14
5: Boundary 1.14/1.15
6: Boundary 1.15/1.16
7: Boundary 1.16/1.17
8: Boundary 1.17/1.18
9: Boundary 1.18/1.19a
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
ENST00000355710
1a
ENSE00001948565
chr10:
43572475-43572779
305
RET_HUMAN
1-25
25
0
-
-
1.2
ENST00000355710
2
ENSE00001365997
chr10:
43595907-43596170
264
RET_HUMAN
25-113
89
0
-
-
1.3
ENST00000355710
3
ENSE00001095923
chr10:
43597790-43598077
288
RET_HUMAN
113-209
97
0
-
-
1.4b
ENST00000355710
4b
ENSE00001095946
chr10:
43600400-43600641
242
RET_HUMAN
209-289
81
0
-
-
1.5b
ENST00000355710
5b
ENSE00001095907
chr10:
43601824-43602019
196
RET_HUMAN
290-355
66
0
-
-
1.6
ENST00000355710
6
ENSE00001095904
chr10:
43604479-43604678
200
RET_HUMAN
355-421
67
0
-
-
1.7
ENST00000355710
7
ENSE00001312192
chr10:
43606655-43606913
259
RET_HUMAN
422-508
87
0
-
-
1.8
ENST00000355710
8
ENSE00001164816
chr10:
43607547-43607672
126
RET_HUMAN
508-550
43
0
-
-
1.9
ENST00000355710
9
ENSE00001164807
chr10:
43608301-43608411
111
RET_HUMAN
550-587
38
0
-
-
1.10
ENST00000355710
10
ENSE00001164798
chr10:
43609004-43609123
120
RET_HUMAN
587-627
41
0
-
-
1.11b
ENST00000355710
11b
ENSE00001164787
chr10:
43609928-43610184
257
RET_HUMAN
627-712
86
1
A:700-712 (gaps)
46
1.12
ENST00000355710
12
ENSE00001095944
chr10:
43612032-43612179
148
RET_HUMAN
713-762
50
1
A:714-762
49
1.13
ENST00000355710
13
ENSE00001164770
chr10:
43613821-43613928
108
RET_HUMAN
762-798
37
1
A:762-798
37
1.14
ENST00000355710
14
ENSE00001164762
chr10:
43614979-43615193
215
RET_HUMAN
798-869
72
1
A:798-869 (gaps)
72
1.15
ENST00000355710
15
ENSE00001239109
chr10:
43615529-43615651
123
RET_HUMAN
870-910
41
1
A:870-910
41
1.16
ENST00000355710
16
ENSE00001095916
chr10:
43617394-43617464
71
RET_HUMAN
911-934
24
1
A:911-934
24
1.17
ENST00000355710
17
ENSE00001164739
chr10:
43619119-43619256
138
RET_HUMAN
934-980
47
1
A:934-980
47
1.18
ENST00000355710
18
ENSE00001164730
chr10:
43620331-43620430
100
RET_HUMAN
980-1013
34
1
A:980-1012
33
1.19a
ENST00000355710
19a
ENSE00001095931
chr10:
43622023-43622170
148
RET_HUMAN
1014-1063
50
0
-
-
1.20
ENST00000355710
20
ENSE00001386034
chr10:
43623560-43625799
2240
RET_HUMAN
1063-1114
52
0
-
-
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2ivua_ (A:)
View:
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(
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Folds
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(
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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
d2ivua_
A:
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2ivuA01 (A:707-806)
2a: CATH_2ivuA02 (A:807-1010)
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(
)
(
)
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
2ivuA01
A:707-806
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
2a
2ivuA02
A:807-1010
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
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