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1OAN
Asym. Unit
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Asym.Unit (138 KB)
Biol.Unit 1 (131 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE PROTEIN
Authors
:
Y. Modis, S. C. Harrison
Date
:
16 Jan 03 (Deposition) - 16 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Glycoprotein, Dengue Virus, Membrane Fusion, Flavivirus, Fusion Peptide, Low-Ph Conformational Change
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Modis, S. Ogata, D. Clements, S. C. Harrison
A Ligand-Binding Pocket In The Dengue Virus Envelope Glycoprotein
Proc. Natl. Acad. Sci. Usa V. 100 6986 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-L-FUCOSE (FUCa)
2b: ALPHA-L-FUCOSE (FUCb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
3
NA
1
Ligand/Ion
SODIUM ION
4
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:67 , MET A:118
BINDING SITE FOR RESIDUE NAG A1396
02
AC2
SOFTWARE
HIS A:149 , ASN A:153 , HIS A:158 , NAG A:1398 , FUC A:1399 , GLY B:102
BINDING SITE FOR RESIDUE NAG A1397
03
AC3
SOFTWARE
NAG A:1397 , FUC A:1399 , BMA A:1400
BINDING SITE FOR RESIDUE NAG A1398
04
AC4
SOFTWARE
GLU A:147 , HIS A:149 , LYS A:157 , NAG A:1397 , NAG A:1398
BINDING SITE FOR RESIDUE FUC A1399
05
AC5
SOFTWARE
NAG A:1398
BINDING SITE FOR RESIDUE BMA A1400
06
AC6
SOFTWARE
ASN B:67 , MET B:118 , HOH B:2025
BINDING SITE FOR RESIDUE NAG B1395
07
AC7
SOFTWARE
GLY A:102 , HIS B:149 , ASN B:153 , HIS B:158 , NAG B:1397 , FUC B:1398 , HOH B:2011
BINDING SITE FOR RESIDUE NAG B1396
08
AC8
SOFTWARE
NAG B:1396 , FUC B:1398 , BMA B:1399
BINDING SITE FOR RESIDUE NAG B1397
09
AC9
SOFTWARE
GLU B:147 , HIS B:149 , LYS B:157 , NAG B:1396 , NAG B:1397
BINDING SITE FOR RESIDUE FUC B1398
10
BC1
SOFTWARE
NAG B:1397
BINDING SITE FOR RESIDUE BMA B1399
11
BC2
SOFTWARE
GLU A:85 , HIS A:94 , HIS A:346
BINDING SITE FOR RESIDUE NA A1395
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1oana1 (A:298-394)
1b: SCOP_d1oanb1 (B:298-394)
2a: SCOP_d1oana2 (A:1-297)
2b: SCOP_d1oanb2 (B:1-297)
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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
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Class II viral fusion proteins C-terminal domain
(27)
Protein domain
:
Envelope glycoprotein
(14)
Dengue virus type 2 [TaxId: 11060]
(9)
1a
d1oana1
A:298-394
1b
d1oanb1
B:298-394
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Viral glycoprotein, central and dimerisation domains
(24)
Superfamily
:
Viral glycoprotein, central and dimerisation domains
(24)
Family
:
Viral glycoprotein, central and dimerisation domains
(17)
Protein domain
:
Envelope glycoprotein
(9)
Dengue virus type 2 [TaxId: 11060]
(7)
2a
d1oana2
A:1-297
2b
d1oanb2
B:1-297
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1oanA02 (A:52-62,A:122-132,A:190-231,A:253-267)
1b: CATH_1oanB02 (B:52-62,B:122-132,B:190-231,B:253-267)
2a: CATH_1oanA03 (A:63-121,A:232-252)
2b: CATH_1oanB03 (B:63-121,B:232-252)
3a: CATH_1oanA04 (A:295-394)
3b: CATH_1oanB04 (B:295-394)
4a: CATH_1oanA01 (A:1-51,A:133-189,A:268-294)
4b: CATH_1oanB01 (B:1-51,B:133-189,B:268-294)
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(
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)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Viral Envelope Glycoprotein; domain 2
(12)
Homologous Superfamily
:
Viral Envelope Glycoprotein, domain 2
(12)
Dengue virus type 2. Organism_taxid: 11060. Strain: strain pr159/s1.
(1)
1a
1oanA02
A:52-62,A:122-132,A:190-231,A:253-267
1b
1oanB02
B:52-62,B:122-132,B:190-231,B:253-267
Topology
:
Viral Envelope Glycoprotein; domain 3
(12)
Homologous Superfamily
:
Viral Envelope Glycoprotein, domain 3
(12)
Dengue virus type 2. Organism_taxid: 11060. Strain: strain pr159/s1.
(1)
2a
1oanA03
A:63-121,A:232-252
2b
1oanB03
B:63-121,B:232-252
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.350, no name defined]
(26)
Dengue virus type 2. Organism_taxid: 11060. Strain: strain pr159/s1.
(1)
3a
1oanA04
A:295-394
3b
1oanB04
B:295-394
Topology
:
Tick-borne Encephalitis virus Glycoprotein; domain 1
(14)
Homologous Superfamily
:
Tick-borne Encephalitis virus Glycoprotein, domain 1
(14)
Dengue virus type 2. Organism_taxid: 11060. Strain: strain pr159/s1.
(1)
4a
1oanA01
A:1-51,A:133-189,A:268-294
4b
1oanB01
B:1-51,B:133-189,B:268-294
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Flavi_glycop_C_1oanB01 (B:298-393)
1b: PFAM_Flavi_glycop_C_1oanB02 (B:298-393)
2a: PFAM_Flavi_glycoprot_1oanB03 (B:1-296)
2b: PFAM_Flavi_glycoprot_1oanB04 (B:1-296)
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Clans
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)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Flavi_glycop_C]
(15)
Family
:
Flavi_glycop_C
(15)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(2)
1a
Flavi_glycop_C-1oanB01
B:298-393
1b
Flavi_glycop_C-1oanB02
B:298-393
Clan
:
no clan defined [family: Flavi_glycoprot]
(10)
Family
:
Flavi_glycoprot
(10)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(2)
2a
Flavi_glycoprot-1oanB03
B:1-296
2b
Flavi_glycoprot-1oanB04
B:1-296
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