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2VWE
Asym. Unit
Info
Asym.Unit (171 KB)
Biol.Unit 1 (165 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF VASCULAR ENDOTHELIAL GROWTH FACTOR-B IN COMPLEX WITH A NEUTRALIZING ANTIBODY FAB FRAGMENT
Authors
:
P. Leonard, P. D. Scotney, T. Jabeen, S. Iyer, L. J. Fabri, A. D. Nash, K. R. Acharya
Date
:
23 Jun 08 (Deposition) - 04 Nov 08 (Release) - 16 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B,C,E,J,L
Biol. Unit 1: A,B,C,E,J,L (1x)
Keywords
:
Immune System, Glycoprotein, Cysteine-Knot, Growth Factor, Vegf-B, Mitogen, Secreted, Angiogenesis, Neutralizing Antibody, Heparin-Binding, Alternative Splicing
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
P. Leonard, P. D. Scotney, T. Jabeen, S. Iyer, L. J. Fabri, A. D. Nash, K. R. Acharya
Crystal Structure Of Vascular Endothelial Growth Factor-B In Complex With A Neutralising Antibody Fab Fragment.
J. Mol. Biol. V. 384 1203 2008
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Hetero Components
(0, 0)
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Sites
(0, 0)
Info
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: PDGF_2 (A:13-108,B:13-108)
2: PDGF_1 (A:49-61,B:49-61)
3: IG_MHC (C:191-197,J:191-197)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDGF_2
PS50278
Platelet-derived growth factor (PDGF) family profile.
VEGFB_HUMAN
34-129
2
A:13-108
B:13-108
2
PDGF_1
PS00249
Platelet-derived growth factor (PDGF) family signature.
VEGFB_HUMAN
70-82
2
A:49-61
B:49-61
3
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_MOUSE
84-90
2
C:191-197
J:191-197
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Exons
(4, 8)
Info
All Exons
Exon 1.2 (A:11-14 | B:11-14)
Exon 1.3 (A:14-79 | B:14-79)
Exon 1.4 (A:80-104 | B:80-104)
Exon 1.5 (A:104-108 | B:104-108)
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6a
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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
ENST00000309422
1
ENSE00001238390
chr11:
64002266-64002365
100
VEGFB_HUMAN
1-20
20
0
-
-
1.2
ENST00000309422
2
ENSE00001238372
chr11:
64002930-64002972
43
VEGFB_HUMAN
21-35
15
2
A:11-14
B:11-14
4
4
1.3
ENST00000309422
3
ENSE00001195939
chr11:
64003285-64003481
197
VEGFB_HUMAN
35-100
66
2
A:14-79
B:14-79
66
66
1.4
ENST00000309422
4
ENSE00001195931
chr11:
64003726-64003799
74
VEGFB_HUMAN
101-125
25
2
A:80-104
B:80-104
25
25
1.5
ENST00000309422
5
ENSE00001195925
chr11:
64004659-64004694
36
VEGFB_HUMAN
125-137
13
2
A:104-108
B:104-108
5
5
1.6a
ENST00000309422
6a
ENSE00001238383
chr11:
64004892-64005127
236
VEGFB_HUMAN
137-207
71
0
-
-
1.7
ENST00000309422
7
ENSE00001786303
chr11:
64005828-64006258
431
VEGFB_HUMAN
-
0
0
-
-
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SCOP Domains
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CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_2vweA00 (A:11-108)
1b: CATH_2vweB00 (B:11-108)
2a: CATH_2vweC02 (C:107-210)
2b: CATH_2vweE02 (E:114-212)
2c: CATH_2vweL02 (L:114-212)
2d: CATH_2vweJ02 (J:107-210)
2e: CATH_2vweE01 (E:1-113)
2f: CATH_2vweL01 (L:1-113)
2g: CATH_2vweC01 (C:1-106A)
2h: CATH_2vweJ01 (J:1-106A)
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)
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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
2vweA00
A:11-108
1b
2vweB00
B:11-108
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
2vweC02
C:107-210
2b
2vweE02
E:114-212
2c
2vweL02
L:114-212
2d
2vweJ02
J:107-210
2e
2vweE01
E:1-113
2f
2vweL01
L:1-113
2g
2vweC01
C:1-106A
2h
2vweJ01
J:1-106A
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDGF_2vweB01 (B:26-103)
1b: PFAM_PDGF_2vweB02 (B:26-103)
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Clan
:
Cystine-knot
(56)
Family
:
PDGF
(19)
Homo sapiens (Human)
(17)
1a
PDGF-2vweB01
B:26-103
1b
PDGF-2vweB02
B:26-103
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Asymmetric Unit 1
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