PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1QTY
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (125 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR
Authors
:
C. Wiesmann, A. M. De Vos
Date
:
29 Jun 99 (Deposition) - 12 Jan 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : R,S,T,U,V,W,X,Y
Biol. Unit 1: V,W,X,Y (1x)
Biol. Unit 2: R,S,T,U (1x)
Biol. Unit 3: R,S,T,U,V,W,X,Y (1x)
Keywords
:
Complex (Growth Factor/Receptor), Flt-1, Vegf Receptor, Receptor Tyrosine Kinase, Cystine Knot, Glycoprotein, Immunoglobulin-Like Domain, I-Set, Hormone/Growth Factor Receptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. A. Starovasnik, H. W. Christinger, C. Wiesmann, M. A. Champe, A. M. De Vos, N. J. Skelton
Solution Structure Of The Vegf-Binding Domain Of Flt-1: Comparison Of Its Free And Bound States.
J. Mol. Biol. V. 293 531 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_042046 (E144K, chain T/U/X/Y, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_042046
E
144
K
VGFR1_HUMAN
Polymorphism
55974987
T/U/X/Y
E
144
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: PDGF_2 (R:13-107,S:13-108,V:13-107,W:13-10...)
2: PDGF_1 (R:49-61,S:49-61,V:49-61,W:49-61)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDGF_2
PS50278
Platelet-derived growth factor (PDGF) family profile.
VEGFA_HUMAN
39-135
4
R:13-107
S:13-108
V:13-107
W:13-107
2
PDGF_1
PS00249
Platelet-derived growth factor (PDGF) family signature.
VEGFA_HUMAN
75-87
4
R:49-61
S:49-61
V:49-61
W:49-61
[
close PROSITE info
]
Exons
(2, 8)
Info
All Exons
Exon 1.4 (T:132-171 | U:132-171 | X:132-171 ...)
Exon 1.5 (T:172-225 | U:172-225 | X:172-225 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5
3: Boundary 1.5/1.6
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
1.1
ENST00000282397
1
ENSE00001249591
chr13:
29069232-29068917
316
VGFR1_HUMAN
1-22
22
0
-
-
1.2
ENST00000282397
2
ENSE00000938500
chr13:
29041754-29041658
97
VGFR1_HUMAN
22-54
33
0
-
-
1.3
ENST00000282397
3
ENSE00000938501
chr13:
29041266-29041040
227
VGFR1_HUMAN
54-130
77
0
-
-
1.4
ENST00000282397
4
ENSE00000906630
chr13:
29012482-29012358
125
VGFR1_HUMAN
130-171
42
4
T:132-171
U:132-171
X:132-171
Y:132-171
40
40
40
40
1.5
ENST00000282397
5
ENSE00000906629
chr13:
29008357-29008195
163
VGFR1_HUMAN
172-226
55
4
T:172-225
U:172-225
X:172-225
Y:172-225
54
54
54
54
1.6
ENST00000282397
6
ENSE00000906628
chr13:
29008092-29007956
137
VGFR1_HUMAN
226-271
46
0
-
-
1.7
ENST00000282397
7
ENSE00000906627
chr13:
29005447-29005273
175
VGFR1_HUMAN
272-330
59
0
-
-
1.8
ENST00000282397
8
ENSE00000906626
chr13:
29004304-29004187
118
VGFR1_HUMAN
330-369
40
0
-
-
1.9
ENST00000282397
9
ENSE00000906625
chr13:
29002058-29001889
170
VGFR1_HUMAN
369-426
58
0
-
-
1.10
ENST00000282397
10
ENSE00000906624
chr13:
29001455-29001296
160
VGFR1_HUMAN
426-479
54
0
-
-
1.11
ENST00000282397
11
ENSE00000679737
chr13:
28980031-28979917
115
VGFR1_HUMAN
479-517
39
0
-
-
1.12
ENST00000282397
12
ENSE00000679735
chr13:
28971205-28971097
109
VGFR1_HUMAN
518-554
37
0
-
-
1.13
ENST00000282397
13
ENSE00001005702
chr13:
28964241-28963933
309
VGFR1_HUMAN
554-657
104
0
-
-
1.14
ENST00000282397
14
ENSE00001005684
chr13:
28959168-28959022
147
VGFR1_HUMAN
657-706
50
0
-
-
1.15
ENST00000282397
15
ENSE00001005678
chr13:
28931822-28931691
132
VGFR1_HUMAN
706-750
45
0
-
-
1.16
ENST00000282397
16
ENSE00001005688
chr13:
28919688-28919582
107
VGFR1_HUMAN
750-785
36
0
-
-
1.17
ENST00000282397
17
ENSE00000679727
chr13:
28913437-28913305
133
VGFR1_HUMAN
786-830
45
0
-
-
1.18
ENST00000282397
18
ENSE00001005682
chr13:
28908266-28908162
105
VGFR1_HUMAN
830-865
36
0
-
-
1.19
ENST00000282397
19
ENSE00000679725
chr13:
28903865-28903752
114
VGFR1_HUMAN
865-903
39
0
-
-
1.20
ENST00000282397
20
ENSE00001005685
chr13:
28901687-28901599
89
VGFR1_HUMAN
903-932
30
0
-
-
1.21
ENST00000282397
21
ENSE00000679723
chr13:
28897083-28896927
157
VGFR1_HUMAN
933-985
53
0
-
-
1.22
ENST00000282397
22
ENSE00000679722
chr13:
28896496-28896399
98
VGFR1_HUMAN
985-1017
33
0
-
-
1.23
ENST00000282397
23
ENSE00001761843
chr13:
28895722-28895600
123
VGFR1_HUMAN
1018-1058
41
0
-
-
1.24
ENST00000282397
24
ENSE00000679720
chr13:
28893671-28893560
112
VGFR1_HUMAN
1059-1096
38
0
-
-
1.25
ENST00000282397
25
ENSE00001005671
chr13:
28891734-28891635
100
VGFR1_HUMAN
1096-1129
34
0
-
-
1.26
ENST00000282397
26
ENSE00001005693
chr13:
28886235-28886130
106
VGFR1_HUMAN
1129-1164
36
0
-
-
1.27
ENST00000282397
27
ENSE00000679717
chr13:
28885869-28885727
143
VGFR1_HUMAN
1165-1212
48
0
-
-
1.28
ENST00000282397
28
ENSE00001005655
chr13:
28883064-28882980
85
VGFR1_HUMAN
1212-1240
29
0
-
-
1.29
ENST00000282397
29
ENSE00000679715
chr13:
28880909-28880815
95
VGFR1_HUMAN
1241-1272
32
0
-
-
1.30
ENST00000282397
30
ENSE00001157319
chr13:
28877505-28874489
3017
VGFR1_HUMAN
1272-1338
67
0
-
-
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1qtyt_ (T:)
1b: SCOP_d1qtyu_ (U:)
1c: SCOP_d1qtyx_ (X:)
1d: SCOP_d1qtyy_ (Y:)
2a: SCOP_d1qtyr_ (R:)
2b: SCOP_d1qtys_ (S:)
2c: SCOP_d1qtyv_ (V:)
2d: SCOP_d1qtyw_ (W:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
I set domains
(152)
Protein domain
:
Second domain of the Flt-1 receptor
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1qtyt_
T:
1b
d1qtyu_
U:
1c
d1qtyx_
X:
1d
d1qtyy_
Y:
Class
:
Small proteins
(3458)
Fold
:
Cystine-knot cytokines
(124)
Superfamily
:
Cystine-knot cytokines
(124)
Family
:
Platelet-derived growth factor-like
(26)
Protein domain
:
Vascular endothelial growth factor, VEGF
(18)
Human (Homo sapiens) [TaxId: 9606]
(16)
2a
d1qtyr_
R:
2b
d1qtys_
S:
2c
d1qtyv_
V:
2d
d1qtyw_
W:
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1qtyS00 (S:13-108)
1b: CATH_1qtyR00 (R:13-107)
1c: CATH_1qtyV00 (V:13-107)
1d: CATH_1qtyW00 (W:13-107)
2a: CATH_1qtyT00 (T:132-225)
2b: CATH_1qtyU00 (U:132-225)
2c: CATH_1qtyX00 (X:132-225)
2d: CATH_1qtyY00 (Y:132-225)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Cystine Knot Cytokines, subunit B
(102)
Homologous Superfamily
:
Cystine-knot cytokines
(102)
Human (Homo sapiens)
(84)
1a
1qtyS00
S:13-108
1b
1qtyR00
R:13-107
1c
1qtyV00
V:13-107
1d
1qtyW00
W:13-107
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
1qtyT00
T:132-225
2b
1qtyU00
U:132-225
2c
1qtyX00
X:132-225
2d
1qtyY00
Y:132-225
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_PDGF_1qtyW01 (W:26-104)
1b: PFAM_PDGF_1qtyW02 (W:26-104)
1c: PFAM_PDGF_1qtyW03 (W:26-104)
1d: PFAM_PDGF_1qtyW04 (W:26-104)
2a: PFAM_Ig_2_1qtyY01 (Y:137-225)
2b: PFAM_Ig_2_1qtyY02 (Y:137-225)
2c: PFAM_Ig_2_1qtyY03 (Y:137-225)
2d: PFAM_Ig_2_1qtyY04 (Y:137-225)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cystine-knot
(56)
Family
:
PDGF
(19)
Homo sapiens (Human)
(17)
1a
PDGF-1qtyW01
W:26-104
1b
PDGF-1qtyW02
W:26-104
1c
PDGF-1qtyW03
W:26-104
1d
PDGF-1qtyW04
W:26-104
Clan
:
Ig
(577)
Family
:
Ig_2
(52)
Homo sapiens (Human)
(39)
2a
Ig_2-1qtyY01
Y:137-225
2b
Ig_2-1qtyY02
Y:137-225
2c
Ig_2-1qtyY03
Y:137-225
2d
Ig_2-1qtyY04
Y:137-225
[
close Pfam info
]
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 R
Chain S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (130 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (125 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1QTY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help