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3NXG
Biol. Unit 2
Info
Asym.Unit (231 KB)
Biol.Unit 1 (225 KB)
Biol.Unit 2 (447 KB)
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(1)
Title
:
JC POLYOMAVIRUS VP1
Authors
:
U. Neu, L. J. Stroeh, T. Stehle
Date
:
13 Jul 10 (Deposition) - 17 Nov 10 (Release) - 17 Nov 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: A,B,C,D,E (2x)
Keywords
:
Beta-Sandwich Jelly Roll, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Neu, M. S. Maginnis, A. S. Palma, L. J. Stroh, C. D. Nelson, T. Feizi, W. J. Atwood, T. Stehle
Structure-Function Analysis Of The Human Jc Polyomavirus Establishes The Lstc Pentasaccharide As A Functional Receptor Motif.
Cell Host Microbe V. 8 309 2010
[
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Hetero Components
(2, 20)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
10
Ligand/Ion
GLYCEROL
[
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]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:62 , SER A:64 , SER A:69 , ASP A:70 , SER A:71 , PRO A:72 , HIS E:121
BINDING SITE FOR RESIDUE GOL A 4
02
AC2
SOFTWARE
HIS A:142 , PHE A:144 , THR A:215 , HOH A:1111
BINDING SITE FOR RESIDUE EDO A 1
03
AC3
SOFTWARE
THR A:234
BINDING SITE FOR RESIDUE EDO A 290
04
AC4
SOFTWARE
HIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , HOH B:698
BINDING SITE FOR RESIDUE GOL B 5
05
AC5
SOFTWARE
HIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , PRO C:72 , HOH C:883
BINDING SITE FOR RESIDUE GOL C 1
06
AC6
SOFTWARE
HIS C:142 , GLY C:214 , THR C:215
BINDING SITE FOR RESIDUE EDO C 290
07
AC7
SOFTWARE
HIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , PRO D:72
BINDING SITE FOR RESIDUE GOL D 2
08
AC8
SOFTWARE
HIS D:142 , PHE D:144 , GLY D:214 , THR D:215 , HOH D:346
BINDING SITE FOR RESIDUE EDO D 1
09
AC9
SOFTWARE
ARG A:265 , ASP B:65 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , HOH E:390 , HOH E:691
BINDING SITE FOR RESIDUE GOL E 3
10
BC1
SOFTWARE
HIS E:142 , PHE E:144 , GLY E:214 , THR E:215
BINDING SITE FOR RESIDUE EDO E 1
[
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SAPs(SNPs)/Variants
(11, 110)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_VP1_POVJC_001 (D65H, chain A/B/C/D/E, )
02: VAR_VP1_POVJC_002 (N73S, chain A/B/C/D/E, )
03: VAR_VP1_POVJC_003 (R74K, chain A/B/C/D/E, )
04: VAR_VP1_POVJC_004 (I112L, chain A/B/C/D/E, )
05: VAR_VP1_POVJC_005 (S116T, chain A/B/C/D/E, )
06: VAR_VP1_POVJC_006 (T127A, chain A/B/C/D/E, )
07: VAR_VP1_POVJC_007 (L157V, chain A/B/C/D/E, )
08: VAR_VP1_POVJC_008 (S266L, chain A/B/C/D/E, )
09: VAR_VP1_POVJC_009 (S268F, chain A/B/C/D/E, )
10: VAR_VP1_POVJC_010 (S268T, chain A/B/C/D/E, )
11: VAR_VP1_POVJC_011 (S268Y, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_VP1_POVJC_001
*
D
66
H
VP1_POVJC
---
---
A/B/C/D/E
D
65
H
02
UniProt
VAR_VP1_POVJC_002
*
N
74
S
VP1_POVJC
---
---
A/B/C/D/E
N
73
S
03
UniProt
VAR_VP1_POVJC_003
*
R
75
K
VP1_POVJC
---
---
A/B/C/D/E
R
74
K
04
UniProt
VAR_VP1_POVJC_004
*
I
113
L
VP1_POVJC
---
---
A/B/C/D/E
I
112
L
05
UniProt
VAR_VP1_POVJC_005
*
S
117
T
VP1_POVJC
---
---
A/B/C/D/E
S
116
T
06
UniProt
VAR_VP1_POVJC_006
*
T
128
A
VP1_POVJC
---
---
A/B/C/D/E
T
127
A
07
UniProt
VAR_VP1_POVJC_007
*
L
158
V
VP1_POVJC
---
---
A/B/C/D/E
L
157
V
08
UniProt
VAR_VP1_POVJC_008
*
S
267
L
VP1_POVJC
---
---
A/B/C/D/E
S
266
L
09
UniProt
VAR_VP1_POVJC_009
*
S
269
F
VP1_POVJC
---
---
A/B/C/D/E
S
268
F
10
UniProt
VAR_VP1_POVJC_010
*
S
269
T
VP1_POVJC
---
---
A/B/C/D/E
S
268
T
11
UniProt
VAR_VP1_POVJC_011
*
S
269
Y
VP1_POVJC
---
---
A/B/C/D/E
S
268
Y
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d3nxga_ (A:)
1b: SCOP_d3nxgb_ (B:)
1c: SCOP_d3nxgc_ (C:)
1d: SCOP_d3nxgd_ (D:)
1e: SCOP_d3nxge_ (E:)
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Protein Domains
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Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Group I dsDNA viruses
(30)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Jc polyomavirus [TaxId: 10632]
(5)
1a
d3nxga_
A:
1b
d3nxgb_
B:
1c
d3nxgc_
C:
1d
d3nxgd_
D:
1e
d3nxge_
E:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Polyoma_coat_3nxgE01 (E:24-289)
1b: PFAM_Polyoma_coat_3nxgE02 (E:24-289)
1c: PFAM_Polyoma_coat_3nxgE03 (E:24-289)
1d: PFAM_Polyoma_coat_3nxgE04 (E:24-289)
1e: PFAM_Polyoma_coat_3nxgE05 (E:24-289)
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Clans
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(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Polyoma_coat]
(8)
Family
:
Polyoma_coat
(8)
JC polyomavirus (JCPyV) (JCV)
(2)
1a
Polyoma_coat-3nxgE01
E:24-289
1b
Polyoma_coat-3nxgE02
E:24-289
1c
Polyoma_coat-3nxgE03
E:24-289
1d
Polyoma_coat-3nxgE04
E:24-289
1e
Polyoma_coat-3nxgE05
E:24-289
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Asym.Unit (231 KB)
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