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3GQI
Asym. Unit
Info
Asym.Unit (96 KB)
Biol.Unit 1 (90 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ACTIVATED RECEPTOR TYROSINE KINASE IN COMPLEX WITH SUBSTRATES
Authors
:
J. H. Bae, E. D. Lew, S. Yuzawa, F. Tome, I. Lax, J. Schlessinger
Date
:
24 Mar 09 (Deposition) - 18 Aug 09 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Phosphorylated Kinase, Py-Recognition, Tandem Sh2 Domains, Atp Analog, Atp-Binding, Craniosynostosis, Disease Mutation, Disulfide Bond, Dwarfism, Glycoprotein, Heparin-Binding, Hypogonadotropic Hypogonadism, Immunoglobulin Domain, Kallmann Syndrome, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Receptor, Transferase, Transmembrane, Tyrosine-Protein Kinase, Hydrolase, Lipid Degradation, Sh2 Domain, Sh3 Domain, Transducer, Transferase- Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Bae, E. D. Lew, S. Yuzawa, F. Tome, I. Lax, J. Schlessinger
The Selectivity Of Receptor Tyrosine Kinase Signaling Is Controlled By A Secondary Sh2 Domain Binding Site.
Cell(Cambridge, Mass. ) V. 138 514 2009
[
close entry info
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Hetero Components
(4, 6)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
2a: DECAVANADATE (DVTa)
3a: MAGNESIUM ION (MGa)
4a: O-PHOSPHOTYROSINE (PTRa)
4b: O-PHOSPHOTYROSINE (PTRb)
4c: O-PHOSPHOTYROSINE (PTRc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACP
1
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
DVT
1
Ligand/Ion
DECAVANADATE
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
PTR
3
Mod. Amino Acid
O-PHOSPHOTYROSINE
[
close Hetero Component info
]
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
ASP A:503 , LYS A:504 , PRO A:505 , ASN A:506 , ARG A:507 , HOH B:34 , LEU B:673 , THR B:674 , ARG B:675 , ARG B:694 , ARG B:696 , ASN B:697 , GLU B:698
BINDING SITE FOR RESIDUE DVT A 1
2
AC2
SOFTWARE
LEU A:484 , GLY A:485 , GLY A:487 , ALA A:488 , PHE A:489 , GLY A:490 , VAL A:492 , ALA A:512 , LYS A:514 , GLU A:562 , ALA A:564 , ASN A:568 , ARG A:627 , ASN A:628 , LEU A:630 , ASP A:641 , MG A:776
BINDING SITE FOR RESIDUE ACP A 775
3
AC3
SOFTWARE
ASN A:628 , ASP A:641 , ACP A:775
BINDING SITE FOR RESIDUE MG A 776
[
close Site info
]
SAPs(SNPs)/Variants
(31, 31)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_069292 (R470L, chain A, )
02: VAR_069956 (P483T, chain A, )
03: VAR_070853 (G490R, chain A, )
04: VAR_030995 (A520T, chain A, )
05: VAR_030996 (I538V, chain A, )
06: VAR_017889 (V607M, chain A, )
07: VAR_069293 (K618N, chain A, )
08: VAR_030997 (H621R, chain A, )
09: VAR_030998 (R622G, chain A, )
10: VAR_030999 (R622Q, chain A, )
11: VAR_070854 (D623Y, chain A, )
12: VAR_071460 (R627T, chain A, )
13: VAR_070855 (N628K, chain A, )
14: VAR_042203 (V664L, chain A, )
15: VAR_017890 (W666R, chain A, )
16: VAR_069957 (E670K, chain A, )
17: VAR_069294 (A671P, chain A, )
18: VAR_031000 (S685F, chain A, )
19: VAR_031001 (G687R, chain A, )
20: VAR_069958 (E692G, chain A, )
21: VAR_031002 (I693F, chain A, )
22: VAR_031003 (G703R, chain A, )
23: VAR_031004 (G703S, chain A, )
24: VAR_017891 (M719R, chain A, )
25: VAR_031005 (P722H, chain A, )
26: VAR_031006 (P722S, chain A, )
27: VAR_031007 (N724K, chain A, )
28: VAR_070856 (C725Y, chain A, )
29: VAR_031008 (P745S, chain A, )
30: VAR_069959 (D768Y, chain A, )
31: VAR_031009 (L769V, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_069292
R
470
L
FGFR1_HUMAN
Disease (HH2)
---
A
R
470
L
02
UniProt
VAR_069956
P
483
T
FGFR1_HUMAN
Disease (HH2)
---
A
P
483
T
03
UniProt
VAR_070853
G
490
R
FGFR1_HUMAN
Disease (HRTFDS)
---
A
G
490
R
04
UniProt
VAR_030995
A
520
T
FGFR1_HUMAN
Disease (HH2)
---
A
A
520
T
05
UniProt
VAR_030996
I
538
V
FGFR1_HUMAN
Disease (HH2)
---
A
I
538
V
06
UniProt
VAR_017889
V
607
M
FGFR1_HUMAN
Disease (HH2)
---
A
V
607
M
07
UniProt
VAR_069293
K
618
N
FGFR1_HUMAN
Disease (HH2)
---
A
K
618
N
08
UniProt
VAR_030997
H
621
R
FGFR1_HUMAN
Disease (HH2)
---
A
H
621
R
09
UniProt
VAR_030998
R
622
G
FGFR1_HUMAN
Disease (HH2)
---
A
R
622
G
10
UniProt
VAR_030999
R
622
Q
FGFR1_HUMAN
Disease (HH2)
---
A
R
622
Q
11
UniProt
VAR_070854
D
623
Y
FGFR1_HUMAN
Disease (HRTFDS)
---
A
D
623
Y
12
UniProt
VAR_071460
R
627
T
FGFR1_HUMAN
Disease (HRTFDS)
---
A
R
627
T
13
UniProt
VAR_070855
N
628
K
FGFR1_HUMAN
Disease (HRTFDS)
---
A
N
628
K
14
UniProt
VAR_042203
V
664
L
FGFR1_HUMAN
Unclassified
---
A
V
664
L
15
UniProt
VAR_017890
W
666
R
FGFR1_HUMAN
Disease (HH2)
---
A
W
666
R
16
UniProt
VAR_069957
E
670
K
FGFR1_HUMAN
Disease (HH2)
---
A
E
670
K
17
UniProt
VAR_069294
A
671
P
FGFR1_HUMAN
Disease (HH2)
---
A
A
671
P
18
UniProt
VAR_031000
S
685
F
FGFR1_HUMAN
Disease (HH2)
---
A
S
685
F
19
UniProt
VAR_031001
G
687
R
FGFR1_HUMAN
Disease (HH2)
---
A
G
687
R
20
UniProt
VAR_069958
E
692
G
FGFR1_HUMAN
Disease (HH2)
---
A
E
692
G
21
UniProt
VAR_031002
I
693
F
FGFR1_HUMAN
Disease (HH2)
---
A
I
693
F
22
UniProt
VAR_031003
G
703
R
FGFR1_HUMAN
Disease (HH2)
---
A
G
703
R
23
UniProt
VAR_031004
G
703
S
FGFR1_HUMAN
Disease (HH2)
---
A
G
703
S
24
UniProt
VAR_017891
M
719
R
FGFR1_HUMAN
Disease (HH2)
---
A
M
719
R
25
UniProt
VAR_031005
P
722
H
FGFR1_HUMAN
Disease (HH2)
---
A
P
722
H
26
UniProt
VAR_031006
P
722
S
FGFR1_HUMAN
Disease (HH2)
---
A
P
722
S
27
UniProt
VAR_031007
N
724
K
FGFR1_HUMAN
Disease (HH2)
---
A
N
724
K
28
UniProt
VAR_070856
C
725
Y
FGFR1_HUMAN
Disease (HRTFDS)
---
A
C
725
Y
29
UniProt
VAR_031008
P
745
S
FGFR1_HUMAN
Disease (HH2)
---
A
P
745
S
30
UniProt
VAR_069959
D
768
Y
FGFR1_HUMAN
Disease (HH2)
---
A
D
768
Y
31
UniProt
VAR_031009
L
769
V
FGFR1_HUMAN
Polymorphism
2956723
A
L
769
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 4)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:484-514)
2: SH2 (B:550-657|B:668-756)
3: PROTEIN_KINASE_TYR (A:619-631)
;
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.
FGFR1_HUMAN
484-514
1
A:484-514
2
SH2
PS50001
Src homology 2 (SH2) domain profile.
PLCG1_RAT
550-657
668-756
2
B:550-657
B:668-756
3
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
FGFR1_HUMAN
619-631
1
A:619-631
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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.
SCOP Domains
(2, 3)
Info
All SCOP Domains
1a: SCOP_d3gqia_ (A:)
2a: SCOP_d3gqib1 (B:545-658)
2b: SCOP_d3gqib2 (B:659-770)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
automated matches
(542)
Human (Homo sapiens) [TaxId: 9606]
(452)
1a
d3gqia_
A:
Fold
:
SH2-like
(260)
Superfamily
:
SH2 domain
(260)
Family
:
SH2 domain
(225)
Protein domain
:
Phospholipase C-gamma-1
(5)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(2)
2a
d3gqib1
B:545-658
2b
d3gqib2
B:659-770
[
close SCOP info
]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3gqiA01 (A:465-563)
2a: CATH_3gqiA02 (A:564-759)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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
3gqiA01
A:465-563
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
3gqiA02
A:564-759
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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(currently selected atoms:
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)
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Nucleic
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