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2PVY
Asym. Unit
Info
Asym.Unit (196 KB)
Biol.Unit 1 (190 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION RESPONSIBLE FOR AN UNCLASSIFIED CRANIOSYNOSTOSIS SYNDROME.
Authors
:
H. Chen, M. Mohammadi
Date
:
10 May 07 (Deposition) - 25 Sep 07 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Kinase Domain Fold Consisting Of N- And C-Lobes, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Chen, J. Ma, W. Li, A. V. Eliseenkova, C. Xu, T. A. Neubert, W. T. Miller, M. Mohammadi
A Molecular Brake In The Kinase Hinge Region Regulates The Activity Of Receptor Tyrosine Kinases.
Mol. Cell V. 27 717 2007
[
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
1b: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPb)
1c: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPc)
1d: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACP
4
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:625 , ARG A:649 , TYR A:657 , THR A:660
BINDING SITE FOR RESIDUE SO4 A 801
2
AC2
SOFTWARE
LEU A:487 , ALA A:515 , VAL A:564 , GLU A:565 , ALA A:567 , ASN A:571 , LEU A:633 , HOH A:932 , HOH A:950 , HOH A:956
BINDING SITE FOR RESIDUE ACP A 802
3
AC3
SOFTWARE
ARG B:625 , ARG B:649 , TYR B:657 , ARG B:664
BINDING SITE FOR RESIDUE SO4 B 8001
4
AC4
SOFTWARE
LEU B:487 , VAL B:495 , ALA B:515 , VAL B:564 , GLU B:565 , TYR B:566 , ALA B:567 , ASN B:571 , ARG B:630 , LEU B:633 , ASP B:644 , HOH B:9041 , HOH B:9047
BINDING SITE FOR RESIDUE ACP B 8002
5
AC5
SOFTWARE
ARG C:625 , ARG C:649 , TYR C:657 , ARG C:664 , HOH C:918
BINDING SITE FOR RESIDUE SO4 C 801
6
AC6
SOFTWARE
LEU C:487 , ALA C:515 , VAL C:564 , GLU C:565 , TYR C:566 , ALA C:567 , ASN C:571 , LEU C:633 , HOH C:938
BINDING SITE FOR RESIDUE ACP C 802
7
AC7
SOFTWARE
ARG D:625 , ARG D:649 , TYR D:657 , THR D:660 , ARG D:664 , HOH D:954
BINDING SITE FOR RESIDUE SO4 D 801
8
AC8
SOFTWARE
LEU D:487 , ALA D:515 , VAL D:564 , GLU D:565 , TYR D:566 , ALA D:567 , ASN D:571 , LEU D:633 , HOH D:956 , HOH D:957
BINDING SITE FOR RESIDUE ACP D 802
[
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SAPs(SNPs)/Variants
(11, 42)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_023788 (K526E, chain A/B/C/D, )
02: VAR_017276 (N549H, chain A/B/C/D, )
03: VAR_017277 (E565G, chain A/B/C/D, )
04: VAR_046071 (R612T, chain A/B/C/D, )
05: VAR_015012 (G613R, chain A/B/C/D, )
06: VAR_029884 (A628T, chain A/B/C/D, )
07: VAR_017278 (K641R, chain A/B/C/D, )
08: VAR_029885 (A648T, chain A/B/C/D, )
09: VAR_017279 (N659N, chain A/D, )
10: VAR_017280 (G663E, chain A/B/C/D, )
11: VAR_017281 (R678G, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_023788
K
526
E
FGFR2_HUMAN
Disease (FSPC)
---
A/B/C/D
K
526
E
02
UniProt
VAR_017276
N
549
H
FGFR2_HUMAN
Disease (CS)
---
A/B/C/D
N
549
H
03
UniProt
VAR_017277
E
565
G
FGFR2_HUMAN
Disease (PS)
---
A/B/C/D
E
565
G
04
UniProt
VAR_046071
R
612
T
FGFR2_HUMAN
Unclassified
---
A/B/C/D
R
612
T
05
UniProt
VAR_015012
G
613
R
FGFR2_HUMAN
Polymorphism
---
A/B/C/D
G
613
R
06
UniProt
VAR_029884
A
628
T
FGFR2_HUMAN
Disease (LADDS)
---
A/B/C/D
A
628
T
07
UniProt
VAR_017278
K
641
R
FGFR2_HUMAN
Disease (PS)
---
A/B/C/D
K
641
R
08
UniProt
VAR_029885
A
648
T
FGFR2_HUMAN
Disease (LADDS)
---
A/B/C/D
A
648
T
09
UniProt
VAR_017279
K
659
N
FGFR2_HUMAN
Unclassified
---
A/D
N
659
N
10
UniProt
VAR_017280
G
663
E
FGFR2_HUMAN
Disease (PS)
---
A/B/C/D
G
663
E
11
UniProt
VAR_017281
R
678
G
FGFR2_HUMAN
Disease (CS)
---
A/B/C/D
R
678
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:487-517,B:487-517,C:487-517,D:48...)
2: PROTEIN_KINASE_TYR (A:622-634,B:622-634,C:622-634,D:62...)
;
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.
FGFR2_HUMAN
487-517
4
A:487-517
B:487-517
C:487-517
D:487-517
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
FGFR2_HUMAN
622-634
4
A:622-634
B:622-634
C:622-634
D:622-634
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.21 (A:467-480 | B:462-480 | C:462-480 ...)
Exon 1.22 (A:480-521 (gaps) | B:480-521 (gaps...)
Exon 1.23 (A:521-558 | B:521-558 | C:521-558 ...)
Exon 1.24 (A:558-621 (gaps) | B:558-621 (gaps...)
Exon 1.25 (A:622-662 | B:622-658 (gaps) | C:6...)
Exon 1.26 (A:663-686 | B:663-686 | C:663-686 ...)
Exon 1.27 (A:686-732 | B:686-732 | C:686-732 ...)
Exon 1.28b (A:732-764 | B:732-764 | C:732-764 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.19c/1.21
2: Boundary 1.21/1.22
3: Boundary 1.22/1.23
4: Boundary 1.23/1.24
5: Boundary 1.24/1.25
6: Boundary 1.25/1.26
7: Boundary 1.26/1.27
8: Boundary 1.27/1.28b
9: Boundary 1.28b/1.31h
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
1.1h
ENST00000358487
1h
ENSE00001816393
chr10:
123357598-123357476
123
FGFR2_HUMAN
-
0
0
-
-
1.3a
ENST00000358487
3a
ENSE00002141262
chr10:
123353481-123353223
259
FGFR2_HUMAN
1-37
37
0
-
-
1.5b
ENST00000358487
5b
ENSE00001099029
chr10:
123325218-123324952
267
FGFR2_HUMAN
37-126
90
0
-
-
1.6a
ENST00000358487
6a
ENSE00001099020
chr10:
123324093-123324016
78
FGFR2_HUMAN
126-152
27
0
-
-
1.7
ENST00000358487
7
ENSE00001295614
chr10:
123310973-123310804
170
FGFR2_HUMAN
152-208
57
0
-
-
1.8
ENST00000358487
8
ENSE00000812216
chr10:
123298229-123298106
124
FGFR2_HUMAN
209-250
42
0
-
-
1.15
ENST00000358487
15
ENSE00001099035
chr10:
123279683-123279493
191
FGFR2_HUMAN
250-313
64
0
-
-
1.18b
ENST00000358487
18b
ENSE00001146218
chr10:
123276977-123276833
145
FGFR2_HUMAN
314-362
49
0
-
-
1.19c
ENST00000358487
19c
ENSE00001448727
chr10:
123274833-123274631
203
FGFR2_HUMAN
362-429
68
0
-
-
1.21
ENST00000358487
21
ENSE00001015834
chr10:
123263455-123263304
152
FGFR2_HUMAN
430-480
51
4
A:467-480
B:462-480
C:462-480
D:467-480
14
19
19
14
1.22
ENST00000358487
22
ENSE00001627890
chr10:
123260461-123260340
122
FGFR2_HUMAN
480-521
42
4
A:480-521 (gaps)
B:480-521 (gaps)
C:480-521 (gaps)
D:480-521 (gaps)
42
42
42
42
1.23
ENST00000358487
23
ENSE00001146272
chr10:
123258119-123258009
111
FGFR2_HUMAN
521-558
38
4
A:521-558
B:521-558
C:521-558
D:521-558
38
38
38
38
1.24
ENST00000358487
24
ENSE00001146264
chr10:
123256236-123256046
191
FGFR2_HUMAN
558-621
64
4
A:558-621 (gaps)
B:558-621 (gaps)
C:558-621 (gaps)
D:558-621 (gaps)
64
64
64
64
1.25
ENST00000358487
25
ENSE00001099037
chr10:
123247627-123247505
123
FGFR2_HUMAN
622-662
41
4
A:622-662
B:622-658 (gaps)
C:622-662 (gaps)
D:622-662
41
37
41
41
1.26
ENST00000358487
26
ENSE00001099030
chr10:
123246938-123246868
71
FGFR2_HUMAN
663-686
24
4
A:663-686
B:663-686
C:663-686
D:663-686
24
24
24
24
1.27
ENST00000358487
27
ENSE00001146235
chr10:
123245046-123244909
138
FGFR2_HUMAN
686-732
47
4
A:686-732
B:686-732
C:686-732
D:686-732
47
47
47
47
1.28b
ENST00000358487
28b
ENSE00002167762
chr10:
123243317-123243212
106
FGFR2_HUMAN
732-767
36
4
A:732-764
B:732-764
C:732-764
D:732-764
33
33
33
33
1.31h
ENST00000358487
31h
ENSE00001847306
chr10:
123239535-123237855
1681
FGFR2_HUMAN
768-821
54
0
-
-
[
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]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2pvya_ (A:)
1b: SCOP_d2pvyb_ (B:)
1c: SCOP_d2pvyc_ (C:)
1d: SCOP_d2pvyd_ (D:)
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Protein Domains
(
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(
)
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
:
Fibroblast growth factor receptor 2
(16)
Human (Homo sapiens) [TaxId: 9606]
(16)
1a
d2pvya_
A:
1b
d2pvyb_
B:
1c
d2pvyc_
C:
1d
d2pvyd_
D:
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2pvyA01 (A:467-566)
1b: CATH_2pvyD01 (D:467-566)
1c: CATH_2pvyB01 (B:462-566)
1d: CATH_2pvyC01 (C:462-566)
2a: CATH_2pvyA02 (A:567-762)
2b: CATH_2pvyD02 (D:567-762)
2c: CATH_2pvyB02 (B:567-762)
2d: CATH_2pvyC02 (C:567-762)
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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
2pvyA01
A:467-566
1b
2pvyD01
D:467-566
1c
2pvyB01
B:462-566
1d
2pvyC01
C:462-566
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
2pvyA02
A:567-762
2b
2pvyD02
D:567-762
2c
2pvyB02
B:567-762
2d
2pvyC02
C:567-762
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Pkinase_Tyr_2pvyD01 (D:481-757)
1b: PFAM_Pkinase_Tyr_2pvyD02 (D:481-757)
1c: PFAM_Pkinase_Tyr_2pvyD03 (D:481-757)
1d: PFAM_Pkinase_Tyr_2pvyD04 (D:481-757)
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Clan
:
PKinase
(934)
Family
:
Pkinase_Tyr
(229)
Homo sapiens (Human)
(202)
1a
Pkinase_Tyr-2pvyD01
D:481-757
1b
Pkinase_Tyr-2pvyD02
D:481-757
1c
Pkinase_Tyr-2pvyD03
D:481-757
1d
Pkinase_Tyr-2pvyD04
D:481-757
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