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2IVU
Biol. Unit 1
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:
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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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close entry info
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Hetero Components
(3, 8)
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
4
Ligand/Ion
FORMIC ACID
2
PTR
2
Mod. Amino Acid
O-PHOSPHOTYROSINE
3
ZD6
2
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
]
SAPs(SNPs)/Variants
(31, 62)
Info
(mutated residues are only available for the asymmetric unit)
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, 4)
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
2
A:730-758
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
RET_HUMAN
870-882
2
A:870-882
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2ivua_ (A:)
View:
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Classes
(
)
(
)
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:
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2ivuA01 (A:707-806)
2a: CATH_2ivuA02 (A:807-1010)
View:
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Classes
(
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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
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Label:
Sorry, no Info available
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