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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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Getting 'PROSITE' information from database.
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Getting 'Exon' information from database.
1EDM
Asym. Unit
Info
Asym.Unit (21 KB)
Biol.Unit 1 (17 KB)
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(1)
Title
:
EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX
Authors
:
Z. Rao, P. Handford, M. Mayhew, V. Knott, G. G. Brownlee, D. Stuart
Date
:
21 Mar 96 (Deposition) - 14 Oct 96 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : B,C
Biol. Unit 1: B,C (1x)
Keywords
:
Crystal Structure, Epidermal Growth Factor, Egf, Calcium- Binding, Egf-Like Domain, Structure And Function, Human Factor Ix, Coagulation Factor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Rao, P. Handford, M. Mayhew, V. Knott, G. G. Brownlee, D. Stuart
The Structure Of A Ca(2+)-Binding Epidermal Growth Factor-Like Domain: Its Role In Protein-Protein Interactions.
Cell(Cambridge, Mass. ) V. 82 131 1995
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
3
Ligand/Ion
CALCIUM 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
SER B:53 , HOH B:204 , HOH B:208 , HOH B:209 , HOH B:210 , HOH B:234 , HOH B:254
BINDING SITE FOR RESIDUE CA B 3
2
AC2
SOFTWARE
ASN B:58 , ASP C:47 , GLY C:48 , GLN C:50 , ASP C:64 , ASP C:65
BINDING SITE FOR RESIDUE CA C 1
3
AC3
SOFTWARE
ASP B:47 , GLY B:48 , GLN B:50 , ASP B:64 , ASP B:65 , ASN C:58
BINDING SITE FOR RESIDUE CA B 2
[
close Site info
]
SAPs(SNPs)/Variants
(18, 36)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006544 (D47G, chain B/C, )
02: VAR_006545 (Q50P, chain B/C, )
03: VAR_006546 (C51S, chain B/C, )
04: VAR_006547 (P55R, chain B/C, )
05: VAR_006548 (C56R, chain B/C, )
06: VAR_017346 (G60D, chain B/C, )
07: VAR_006549 (G60S, chain B/C, )
08: VAR_006550 (C62S, chain B/C, )
09: VAR_006551 (D64N, chain B/C, )
10: VAR_006552 (I66S, chain B/C, )
11: VAR_006553 (N67K, chain B/C, )
12: VAR_006554 (Y69C, chain B/C, )
13: VAR_006555 (C73F, chain B/C, )
14: VAR_006556 (C73R, chain B/C, )
15: VAR_017347 (E78K, chain B/C, )
16: VAR_006557 (G79E, chain B/C, )
17: VAR_017348 (G79R, chain B/C, )
18: VAR_006558 (G79V, chain B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006544
D
93
G
FA9_HUMAN
Disease (HEMB)
---
B/C
D
47
G
02
UniProt
VAR_006545
Q
96
P
FA9_HUMAN
Disease (HEMB)
---
B/C
Q
50
P
03
UniProt
VAR_006546
C
97
S
FA9_HUMAN
Disease (HEMB)
---
B/C
C
51
S
04
UniProt
VAR_006547
P
101
R
FA9_HUMAN
Disease (HEMB)
---
B/C
P
55
R
05
UniProt
VAR_006548
C
102
R
FA9_HUMAN
Disease (HEMB)
---
B/C
C
56
R
06
UniProt
VAR_017346
G
106
D
FA9_HUMAN
Disease (HEMB)
---
B/C
G
60
D
07
UniProt
VAR_006549
G
106
S
FA9_HUMAN
Disease (HEMB)
---
B/C
G
60
S
08
UniProt
VAR_006550
C
108
S
FA9_HUMAN
Disease (HEMB)
---
B/C
C
62
S
09
UniProt
VAR_006551
D
110
N
FA9_HUMAN
Disease (HEMB)
---
B/C
D
64
N
10
UniProt
VAR_006552
I
112
S
FA9_HUMAN
Disease (HEMB)
---
B/C
I
66
S
11
UniProt
VAR_006553
N
113
K
FA9_HUMAN
Disease (HEMB)
---
B/C
N
67
K
12
UniProt
VAR_006554
Y
115
C
FA9_HUMAN
Disease (HEMB)
---
B/C
Y
69
C
13
UniProt
VAR_006555
C
119
F
FA9_HUMAN
Disease (HEMB)
---
B/C
C
73
F
14
UniProt
VAR_006556
C
119
R
FA9_HUMAN
Disease (HEMB)
---
B/C
C
73
R
15
UniProt
VAR_017347
E
124
K
FA9_HUMAN
Disease (HEMB)
---
B/C
E
78
K
16
UniProt
VAR_006557
G
125
E
FA9_HUMAN
Disease (HEMB)
---
B/C
G
79
E
17
UniProt
VAR_017348
G
125
R
FA9_HUMAN
Disease (HEMB)
---
B/C
G
79
R
18
UniProt
VAR_006558
G
125
V
FA9_HUMAN
Disease (HEMB)
---
B/C
G
79
V
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 8)
Info
All PROSITE Patterns/Profiles
1: EGF_3 (B:47-83,C:47-83)
2: EGF_CA (B:47-71,C:47-71)
3: ASX_HYDROXYL (B:62-73,C:62-73)
4: EGF_1 (B:71-82,C:71-82)
5: EGF_2 (B:71-82,C:71-82|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_3
PS50026
EGF-like domain profile.
FA9_HUMAN
93-129
2
B:47-83
C:47-83
2
EGF_CA
PS01187
Calcium-binding EGF-like domain signature.
FA9_HUMAN
93-117
2
B:47-71
C:47-71
3
ASX_HYDROXYL
PS00010
Aspartic acid and asparagine hydroxylation site.
FA9_HUMAN
108-119
2
B:62-73
C:62-73
4
EGF_1
PS00022
EGF-like domain signature 1.
FA9_HUMAN
117-128
2
B:71-82
C:71-82
5
EGF_2
PS01186
EGF-like domain signature 2.
FA9_HUMAN
117-128
155-170
2
B:71-82
C:71-82
-
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.3 (B:46-47 | C:46-47)
Exon 1.4a (B:47-84 | C:47-84)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2b/1.3
2: Boundary 1.3/1.4a
3: Boundary 1.4a/1.5b
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
1.1b
ENST00000218099
1b
ENSE00002195519
X:138612917-138613011
95
FA9_HUMAN
1-30
30
0
-
-
1.2b
ENST00000218099
2b
ENSE00000677287
X:138619169-138619332
164
FA9_HUMAN
30-84
55
0
-
-
1.3
ENST00000218099
3
ENSE00001173335
X:138619521-138619545
25
FA9_HUMAN
85-93
9
2
B:46-47
C:46-47
2
2
1.4a
ENST00000218099
4a
ENSE00001173327
X:138623235-138623348
114
FA9_HUMAN
93-131
39
2
B:47-84
C:47-84
38
38
1.5b
ENST00000218099
5b
ENSE00001173320
X:138630522-138630650
129
FA9_HUMAN
131-174
44
0
-
-
1.6
ENST00000218099
6
ENSE00001173315
X:138633221-138633423
203
FA9_HUMAN
174-241
68
0
-
-
1.7
ENST00000218099
7
ENSE00001173311
X:138642900-138643014
115
FA9_HUMAN
242-280
39
0
-
-
1.8b
ENST00000218099
8b
ENSE00001029145
X:138643683-138645617
1935
FA9_HUMAN
280-461
182
0
-
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1edmb_ (B:)
1b: SCOP_d1edmc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
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(
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Superfamilies
(
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(
)
Families
(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Factor IX (IXa)
(8)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1edmb_
B:
1b
d1edmc_
C:
[
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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]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain B
Chain C
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