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Getting 'Biological Unit' information from database.
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Getting 'Exon' information from database.
2VSM
Asym. Unit
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Asym.Unit (115 KB)
Biol.Unit 1 (109 KB)
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(1)
Title
:
NIPAH VIRUS ATTACHMENT GLYCOPROTEIN IN COMPLEX WITH HUMAN CELL SURFACE RECEPTOR EPHRINB2
Authors
:
T. A. Bowden, A. R. Aricescu, R. J. Gilbert, J. M. Grimes, E. Y. Jones, D. I. Stuart
Date
:
25 Apr 08 (Deposition) - 20 May 08 (Release) - 28 Apr 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Developmental Protein, Henipavirus, Neurogenesis, Glycoprotein, Paramyxovirus, Envelope Protein, Cell Surface Receptor, Hendra, Virion, Ephrin, Complex, Membrane, Hydrolase, B2, Efn, Niv, Eph, Hev, Hev-G, Nipah, Virus, Niv-G, Phosphoprotein, Differentiation, Viral Attachment, Signal-Anchor, Hemagglutinin, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. A. Bowden, A. R. Aricescu, R. J. Gilbert, J. M. Grimes, E. Y. Jones, D. I. Stuart
Structural Basis Of Nipah And Hendra Virus Attachment To Their Cell-Surface Receptor Ephrin-B2
Nat. Struct. Mol. Biol. V. 15 567 2008
[
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: ISOPROPYL ALCOHOL (IPAa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IPA
1
Ligand/Ion
ISOPROPYL ALCOHOL
2
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:454 , THR A:462 , ILE A:464 , SER A:486 , ASN A:509 , HOH A:2495 , HOH A:2496
BINDING SITE FOR RESIDUE IPA A1604
2
AC2
SOFTWARE
THR A:361 , LYS A:415 , ASN A:417 , SER A:419 , LYS A:569 , HOH A:2232 , HOH A:2311
BINDING SITE FOR RESIDUE NAG A1605
3
AC3
SOFTWARE
ASN A:529 , HOH A:2386 , HOH A:2387 , HOH A:2497
BINDING SITE FOR RESIDUE NAG A1606
4
AC4
SOFTWARE
ASN A:478 , TRP A:479 , ARG A:480 , ASN A:481 , HOH A:2366 , HOH A:2368 , HOH A:2499
BINDING SITE FOR RESIDUE NAG A1607
5
AC5
SOFTWARE
ILE A:517 , ASN B:39 , SER B:40 , SER B:41 , LYS B:67 , VAL B:73 , GLY B:74 , GLU B:77 , HOH B:2046 , HOH B:2205
BINDING SITE FOR RESIDUE NAG B1171
[
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SAPs(SNPs)/Variants
(8, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_GLYCP_NIPAV_004 (R248K, chain A, )
2: VAR_GLYCP_NIPAV_005 (T272A, chain A, )
3: VAR_GLYCP_NIPAV_006 (G327D, chain A, )
4: VAR_GLYCP_NIPAV_007 (I408V, chain A, )
5: VAR_GLYCP_NIPAV_008 (V426I, chain A, )
6: VAR_GLYCP_NIPAV_009 (L470Q, chain A, )
7: VAR_GLYCP_NIPAV_010 (N478S, chain A, )
8: VAR_GLYCP_NIPAV_011 (N481D, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_GLYCP_NIPAV_004
*
R
248
K
GLYCP_NIPAV
---
---
A
R
248
K
2
UniProt
VAR_GLYCP_NIPAV_005
*
T
272
A
GLYCP_NIPAV
---
---
A
T
272
A
3
UniProt
VAR_GLYCP_NIPAV_006
*
G
327
D
GLYCP_NIPAV
---
---
A
G
327
D
4
UniProt
VAR_GLYCP_NIPAV_007
*
I
408
V
GLYCP_NIPAV
---
---
A
I
408
V
5
UniProt
VAR_GLYCP_NIPAV_008
*
V
426
I
GLYCP_NIPAV
---
---
A
V
426
I
6
UniProt
VAR_GLYCP_NIPAV_009
*
L
470
Q
GLYCP_NIPAV
---
---
A
L
470
Q
7
UniProt
VAR_GLYCP_NIPAV_010
*
N
478
S
GLYCP_NIPAV
---
---
A
N
478
S
8
UniProt
VAR_GLYCP_NIPAV_011
*
N
481
D
GLYCP_NIPAV
---
---
A
N
481
D
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: EPHRIN_RBD_2 (B:31-167)
2: EPHRIN_RBD_1 (B:112-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EPHRIN_RBD_2
PS51551
Ephrin receptor-binding (ephrin RBD) domain profile.
EFNB2_HUMAN
28-164
1
B:31-167
2
EPHRIN_RBD_1
PS01299
Ephrin receptor-binding (ephrin RBD) domain signature.
EFNB2_HUMAN
109-136
1
B:112-139
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.1a (B:31-44)
Exon 1.2 (B:44-139 (gaps))
Exon 1.3 (B:139-170)
Exon 1.4 (B:170-170)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5b
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
1.1a
ENST00000245323
1a
ENSE00001931658
chr13:
107187462-107187191
272
EFNB2_HUMAN
1-41
41
1
B:31-44
14
1.2
ENST00000245323
2
ENSE00001654984
chr13:
107165160-107164877
284
EFNB2_HUMAN
41-136
96
1
B:44-139 (gaps)
96
1.3
ENST00000245323
3
ENSE00000995278
chr13:
107148188-107148096
93
EFNB2_HUMAN
136-167
32
1
B:139-170
32
1.4
ENST00000245323
4
ENSE00000854052
chr13:
107147342-107147229
114
EFNB2_HUMAN
167-205
39
1
B:170-170
1
1.5b
ENST00000245323
5b
ENSE00001923391
chr13:
107145776-107142093
3684
EFNB2_HUMAN
205-333
129
0
-
-
[
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]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2vsmb_ (B:)
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Protein Domains
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Organisms
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)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Ephrin ectodomain
(11)
Protein domain
:
automated matches
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2vsmb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 2)
Info
all PFAM domains
1a: PFAM_Ephrin_2vsmB01 (B:31-168)
2a: PFAM_HN_2vsmA01 (A:188-601)
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Clans
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Families
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(
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Organisms
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)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Ephrin
(10)
Homo sapiens (Human)
(7)
1a
Ephrin-2vsmB01
B:31-168
Clan
:
Sialidase
(56)
Family
:
HN
(6)
Nipah virus
(2)
2a
HN-2vsmA01
A:188-601
[
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