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3OJM
Asym. Unit
Info
Asym.Unit (65 KB)
Biol.Unit 1 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF FGF1 COMPLEXED WITH THE ECTODOMAIN OF FGFR2B HARBORING P253R APERT MUTATION
Authors
:
A. Beenken, M. Mohammadi
Date
:
23 Aug 10 (Deposition) - 31 Aug 11 (Release) - 07 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Beta Trefoil Motif, Immunoglobulin-Like Domain, Growth Factor, Growth Factor Receptor, Extracellular, Cytokine-Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Beenken, A. V. Eliseenkova, O. A. Ibrahimi, S. K. Olsen, M. Mohammad
Plasticity In Interactions Of Fibroblast Growth Factor 1 (Fgf1) N Terminus With Fgf Receptors Underlies Promiscuity Of Fgf1.
J. Biol. Chem. V. 287 3067 2012
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
3
Ligand/Ion
SULFATE ION
[
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
LYS A:127 , LYS A:133 , ARG A:137 , HOH A:459
BINDING SITE FOR RESIDUE SO4 A 300
2
AC2
SOFTWARE
ASN A:33 , LYS A:127 , LYS A:128 , LYS A:133 , HOH A:456
BINDING SITE FOR RESIDUE SO4 A 301
3
AC3
SOFTWARE
ARG A:39 , HOH A:433 , GLN B:259 , LYS B:279
BINDING SITE FOR RESIDUE SO4 B 370
[
close Site info
]
SAPs(SNPs)/Variants
(48, 48)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_021357 (G21E, chain A, )
02: VAR_017259 (A172F, chain B, )
03: VAR_017260 (M186T, chain B, )
04: VAR_036380 (R203C, chain B, )
05: VAR_004114 (S252F, chain B, )
06: VAR_004113 (S252L, chain B, )
07: VAR_004115 (S252W, chain B, )
08: VAR_004117 (R253R, chain B, )
09: VAR_017261 (P263L, chain B, )
10: VAR_004118 (S267P, chain B, )
11: VAR_042205 (G272V, chain B, )
12: VAR_004120 (F276V, chain B, )
13: VAR_004121 (C278F, chain B, )
14: VAR_017263 (C278Y, chain B, )
15: VAR_017264 (Y281C, chain B, )
16: VAR_042206 (D283N, chain B, )
17: VAR_017265 (I288S, chain B, )
18: VAR_004123 (Q289P, chain B, )
19: VAR_004124 (W290C, chain B, )
20: VAR_017266 (W290G, chain B, )
21: VAR_004125 (W290R, chain B, )
22: VAR_004126 (K292E, chain B, )
23: VAR_004127 (Y301C, chain B, )
24: VAR_004128 (H314S, chain B, )
25: VAR_017267 (S315S, chain B, )
26: VAR_004129 (N321A, chain B, )
27: VAR_004130 (A326C, chain B, )
28: VAR_004131 (N329I, chain B, )
29: VAR_017268 (A335P, chain B, )
30: VAR_004133 (G336E, chain B, )
31: VAR_015011 (G336R, chain B, )
32: VAR_017269 (Y338C, chain B, )
33: VAR_004134 (Y338H, chain B, )
34: VAR_004135 (I339P, chain B, )
35: VAR_004136 (C340F, chain B, )
36: VAR_017270 (C340G, chain B, )
37: VAR_004137 (C340R, chain B, )
38: VAR_004138 (C340S, chain B, )
39: VAR_017271 (C340W, chain B, )
40: VAR_004139 (C340Y, chain B, )
41: VAR_004140 (V342G, chain B, )
42: VAR_004141 (V342P, chain B, )
43: VAR_004142 (Y345C, chain B, )
44: VAR_004143 (A349C, chain B, )
45: VAR_004144 (S352C, chain B, )
46: VAR_017272 (S352Y, chain B, )
47: VAR_004146 (V357F, chain B, )
48: VAR_017273 (K360S, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_021357
G
21
E
FGF1_HUMAN
Polymorphism
17223632
A
G
21
E
02
UniProt
VAR_017259
A
172
F
FGFR2_HUMAN
Disease (PS)
---
B
A
172
F
03
UniProt
VAR_017260
M
186
T
FGFR2_HUMAN
Polymorphism
755793
B
M
186
T
04
UniProt
VAR_036380
R
203
C
FGFR2_HUMAN
Unclassified
---
B
R
203
C
05
UniProt
VAR_004114
S
252
F
FGFR2_HUMAN
Disease (APRS)
---
B
S
252
F
06
UniProt
VAR_004113
S
252
L
FGFR2_HUMAN
Disease (CS)
---
B
S
252
L
07
UniProt
VAR_004115
S
252
W
FGFR2_HUMAN
Disease (PS)
---
B
S
252
W
08
UniProt
VAR_004117
P
253
R
FGFR2_HUMAN
Disease (APRS)
---
B
R
253
R
09
UniProt
VAR_017261
P
263
L
FGFR2_HUMAN
Disease (CS)
---
B
P
263
L
10
UniProt
VAR_004118
S
267
P
FGFR2_HUMAN
Disease (CS)
---
B
S
267
P
11
UniProt
VAR_042205
G
272
V
FGFR2_HUMAN
Unclassified
---
B
G
272
V
12
UniProt
VAR_004120
F
276
V
FGFR2_HUMAN
Disease (CS)
---
B
F
276
V
13
UniProt
VAR_004121
C
278
F
FGFR2_HUMAN
Disease (PS)
---
B
C
278
F
14
UniProt
VAR_017263
C
278
Y
FGFR2_HUMAN
Disease (CS)
---
B
C
278
Y
15
UniProt
VAR_017264
Y
281
C
FGFR2_HUMAN
Disease (CS)
---
B
Y
281
C
16
UniProt
VAR_042206
D
283
N
FGFR2_HUMAN
Unclassified
---
B
D
283
N
17
UniProt
VAR_017265
I
288
S
FGFR2_HUMAN
Disease (CS)
---
B
I
288
S
18
UniProt
VAR_004123
Q
289
P
FGFR2_HUMAN
Disease (JWS)
---
B
Q
289
P
19
UniProt
VAR_004124
W
290
C
FGFR2_HUMAN
Disease (PS)
---
B
W
290
C
20
UniProt
VAR_017266
W
290
G
FGFR2_HUMAN
Disease (CS)
---
B
W
290
G
21
UniProt
VAR_004125
W
290
R
FGFR2_HUMAN
Disease (CS)
---
B
W
290
R
22
UniProt
VAR_004126
K
292
E
FGFR2_HUMAN
Disease (CS)
---
B
K
292
E
23
UniProt
VAR_004127
Y
301
C
FGFR2_HUMAN
Disease (CS)
---
B
Y
301
C
24
UniProt
VAR_004128
A
314
S
FGFR2_HUMAN
Unclassified
---
B
H
314
S
25
UniProt
VAR_017267
A
315
S
FGFR2_HUMAN
Unclassified
---
B
S
315
S
26
UniProt
VAR_004129
D
321
A
FGFR2_HUMAN
Disease (PS)
---
B
N
321
A
27
UniProt
VAR_004130
Y
328
C
FGFR2_HUMAN
Disease (CS)
---
B
A
326
C
28
UniProt
VAR_004131
N
331
I
FGFR2_HUMAN
Disease (CS)
---
B
N
329
I
29
UniProt
VAR_017268
A
337
P
FGFR2_HUMAN
Disease (CS)
---
B
A
335
P
30
UniProt
VAR_004133
G
338
E
FGFR2_HUMAN
Disease (CS)
---
B
G
336
E
31
UniProt
VAR_015011
G
338
R
FGFR2_HUMAN
Disease (CS)
---
B
G
336
R
32
UniProt
VAR_017269
Y
340
C
FGFR2_HUMAN
Disease (PS)
---
B
Y
338
C
33
UniProt
VAR_004134
Y
340
H
FGFR2_HUMAN
Disease (CS)
---
B
Y
338
H
34
UniProt
VAR_004135
T
341
P
FGFR2_HUMAN
Disease (PS)
---
B
I
339
P
35
UniProt
VAR_004136
C
342
F
FGFR2_HUMAN
Disease (CS)
---
B
C
340
F
36
UniProt
VAR_017270
C
342
G
FGFR2_HUMAN
Disease (PS)
---
B
C
340
G
37
UniProt
VAR_004137
C
342
R
FGFR2_HUMAN
Disease (PS)
---
B
C
340
R
38
UniProt
VAR_004138
C
342
S
FGFR2_HUMAN
Disease (PS)
---
B
C
340
S
39
UniProt
VAR_017271
C
342
W
FGFR2_HUMAN
Disease (CS)
---
B
C
340
W
40
UniProt
VAR_004139
C
342
Y
FGFR2_HUMAN
Disease (PS)
---
B
C
340
Y
41
UniProt
VAR_004140
A
344
G
FGFR2_HUMAN
Disease (JWS)
---
B
V
342
G
42
UniProt
VAR_004141
A
344
P
FGFR2_HUMAN
Disease (PS)
---
B
V
342
P
43
UniProt
VAR_004142
S
347
C
FGFR2_HUMAN
Disease (CS)
---
B
Y
345
C
44
UniProt
VAR_004143
S
351
C
FGFR2_HUMAN
Disease (PS)
---
B
A
349
C
45
UniProt
VAR_004144
S
354
C
FGFR2_HUMAN
Disease (CS)
---
B
S
352
C
46
UniProt
VAR_017272
S
354
Y
FGFR2_HUMAN
Disease (CS)
---
B
S
352
Y
47
UniProt
VAR_004146
V
359
F
FGFR2_HUMAN
Disease (PS)
---
B
V
357
F
48
UniProt
VAR_017273
A
362
S
FGFR2_HUMAN
Disease (CS)
---
B
K
360
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: HBGF_FGF (A:86-109)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HBGF_FGF
PS00247
HBGF/FGF family signature.
FGF1_HUMAN
86-109
1
A:86-109
[
close PROSITE info
]
Exons
(9, 9)
Info
All Exons
Exon 1.6a (B:151-152)
Exon 1.7 (B:152-208)
Exon 1.8 (B:209-250)
Exon 1.15 (B:250-313)
Exon 1.18b (B:314-360 (gaps))
Exon 1.19c (B:360-361)
Exon 2.8b (A:10-57)
Exon 2.9b (A:57-91)
Exon 2.10f (A:92-154)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.5b/1.6a
02: Boundary 1.6a/1.7
03: Boundary 1.7/1.8
04: Boundary 1.8/1.15
05: Boundary 1.15/1.18b
06: Boundary 1.18b/1.19c
07: Boundary 1.19c/1.21
08: Boundary 2.3/2.8b
09: Boundary 2.8b/2.9b
10: Boundary 2.9b/2.10f
11: Boundary 2.10f/-
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
1
B:151-152
2
1.7
ENST00000358487
7
ENSE00001295614
chr10:
123310973-123310804
170
FGFR2_HUMAN
152-208
57
1
B:152-208
57
1.8
ENST00000358487
8
ENSE00000812216
chr10:
123298229-123298106
124
FGFR2_HUMAN
209-250
42
1
B:209-250
42
1.15
ENST00000358487
15
ENSE00001099035
chr10:
123279683-123279493
191
FGFR2_HUMAN
250-313
64
1
B:250-313
64
1.18b
ENST00000358487
18b
ENSE00001146218
chr10:
123276977-123276833
145
FGFR2_HUMAN
314-362
49
1
B:314-360 (gaps)
49
1.19c
ENST00000358487
19c
ENSE00001448727
chr10:
123274833-123274631
203
FGFR2_HUMAN
362-429
68
1
B:360-361
2
1.21
ENST00000358487
21
ENSE00001015834
chr10:
123263455-123263304
152
FGFR2_HUMAN
430-480
51
0
-
-
1.22
ENST00000358487
22
ENSE00001627890
chr10:
123260461-123260340
122
FGFR2_HUMAN
480-521
42
0
-
-
1.23
ENST00000358487
23
ENSE00001146272
chr10:
123258119-123258009
111
FGFR2_HUMAN
521-558
38
0
-
-
1.24
ENST00000358487
24
ENSE00001146264
chr10:
123256236-123256046
191
FGFR2_HUMAN
558-621
64
0
-
-
1.25
ENST00000358487
25
ENSE00001099037
chr10:
123247627-123247505
123
FGFR2_HUMAN
622-662
41
0
-
-
1.26
ENST00000358487
26
ENSE00001099030
chr10:
123246938-123246868
71
FGFR2_HUMAN
663-686
24
0
-
-
1.27
ENST00000358487
27
ENSE00001146235
chr10:
123245046-123244909
138
FGFR2_HUMAN
686-732
47
0
-
-
1.28b
ENST00000358487
28b
ENSE00002167762
chr10:
123243317-123243212
106
FGFR2_HUMAN
732-767
36
0
-
-
1.31h
ENST00000358487
31h
ENSE00001847306
chr10:
123239535-123237855
1681
FGFR2_HUMAN
768-821
54
0
-
-
2.3
ENST00000378046
3
ENSE00001476010
chr5:
142065237-142065079
159
FGF1_HUMAN
-
0
0
-
-
2.8b
ENST00000378046
8b
ENSE00002155500
chr5:
141993726-141993524
203
FGF1_HUMAN
1-57
57
1
A:10-57
48
2.9b
ENST00000378046
9b
ENSE00000766692
chr5:
141980370-141980267
104
FGF1_HUMAN
57-91
35
1
A:57-91
35
2.10f
ENST00000378046
10f
ENSE00001476009
chr5:
141975049-141972934
2116
FGF1_HUMAN
92-155
64
1
A:92-154
63
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3ojma_ (A:)
2a: SCOP_d3ojmb2 (B:251-361)
3a: SCOP_d3ojmb1 (B:151-250)
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(
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(
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Cytokine
(169)
Family
:
Fibroblast growth factors (FGF)
(120)
Protein domain
:
Acidic FGF (FGF1)
(88)
Human (Homo sapiens) [TaxId: 9606]
(84)
1a
d3ojma_
A:
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
2a
d3ojmb2
B:251-361
Family
:
I set domains
(152)
Protein domain
:
automated matches
(23)
Human (Homo sapiens) [TaxId: 9606]
(22)
3a
d3ojmb1
B:151-250
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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