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3BWR
Asym. Unit
Info
Asym.Unit (235 KB)
Biol.Unit 1 (229 KB)
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(1)
Title
:
SV40 VP1 PENTAMER IN COMPLEX WITH GM1 OLIGOSACCHARIDE
Authors
:
U. Neu, T. Stehle
Date
:
10 Jan 08 (Deposition) - 04 Mar 08 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Sv40, Gm1, Viral Receptor, Viral Attachment, Ganglioside, Vp1, Polyomaviruses, Capsid Protein, Late Protein, Nucleus, Virion, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Neu, K. Woellner, G. Gauglitz, T. Stehle
Structural Basis Of Gm1 Ganglioside Recognition By Simian Virus 40.
Proc. Natl. Acad. Sci. Usa V. 105 5219 2008
[
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]
Hetero Components
(5, 21)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
3d: BETA-D-GALACTOSE (GALd)
3e: BETA-D-GALACTOSE (GALe)
3f: BETA-D-GALACTOSE (GALf)
4a: N-ACETYL-D-GALACTOSAMINE (NGAa)
4b: N-ACETYL-D-GALACTOSAMINE (NGAb)
4c: N-ACETYL-D-GALACTOSAMINE (NGAc)
5a: O-SIALIC ACID (SIAa)
5b: O-SIALIC ACID (SIAb)
5c: O-SIALIC ACID (SIAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
3
Ligand/Ion
BETA-D-GLUCOSE
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
GAL
6
Ligand/Ion
BETA-D-GALACTOSE
4
NGA
3
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
5
SIA
3
Ligand/Ion
O-SIALIC ACID
[
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Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC5 (SOFTWARE)
05: AC6 (SOFTWARE)
06: AC7 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC2 (SOFTWARE)
10: BC3 (SOFTWARE)
11: BC4 (SOFTWARE)
12: BC5 (SOFTWARE)
13: BC6 (SOFTWARE)
14: BC7 (SOFTWARE)
15: BC8 (SOFTWARE)
16: BC9 (SOFTWARE)
17: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:62 , LYS A:67 , SER A:68 , ASN A:272 , SER A:274 , THR A:276 , GLN A:278 , HOH A:341 , HOH A:439 , HOH A:460 , PHE B:75
BINDING SITE FOR RESIDUE SIA A 298
02
AC2
SOFTWARE
SER A:68 , LEU A:69 , GLN A:84 , THR A:276 , ASN E:138 , HOH E:377 , HOH E:466
BINDING SITE FOR RESIDUE GAL A 299
03
AC3
SOFTWARE
SER A:68 , SER A:274 , HOH A:341
BINDING SITE FOR RESIDUE NGA A 300
04
AC5
SOFTWARE
GLN C:62 , LYS C:67 , SER C:68 , ASN C:272 , SER C:274 , THR C:276 , GLN C:278 , HOH C:314 , HOH C:406 , HOH C:425 , PHE D:75
BINDING SITE FOR RESIDUE SIA C 298
05
AC6
SOFTWARE
ASN B:138 , SER C:68 , LEU C:69 , GLN C:84 , THR C:276 , HOH C:373
BINDING SITE FOR RESIDUE GAL C 299
06
AC7
SOFTWARE
SER C:68 , SER C:274 , HOH C:373 , HOH C:425
BINDING SITE FOR RESIDUE NGA C 300
07
AC9
SOFTWARE
PHE A:75 , GLN E:62 , LYS E:67 , SER E:68 , ASN E:272 , SER E:274 , THR E:276 , GLN E:278 , HOH E:348 , HOH E:357 , HOH E:363 , HOH E:380 , HOH E:458
BINDING SITE FOR RESIDUE SIA E 298
08
BC1
SOFTWARE
ASN D:138 , HOH D:453 , SER E:68 , LEU E:69 , ALA E:70 , GLN E:84 , THR E:276 , HOH E:356 , HOH E:498
BINDING SITE FOR RESIDUE GAL E 299
09
BC2
SOFTWARE
SER E:68 , SER E:274 , HOH E:348 , HOH E:399
BINDING SITE FOR RESIDUE NGA E 300
10
BC3
SOFTWARE
HOH E:474
BINDING SITE FOR RESIDUE GAL E 301
11
BC4
SOFTWARE
HOH E:474
BINDING SITE FOR RESIDUE BGC E 302
12
BC5
SOFTWARE
LEU A:65 , LYS A:280 , HOH A:465 , PHE B:75 , ALA B:166 , HOH B:335
BINDING SITE FOR RESIDUE EDO B 1
13
BC6
SOFTWARE
LEU C:65 , LYS C:280 , HOH C:329 , HOH C:369 , PHE D:75 , ALA D:166
BINDING SITE FOR RESIDUE EDO C 2
14
BC7
SOFTWARE
PHE A:75 , ALA A:166 , HOH A:315 , HOH A:375 , LEU E:65 , ILE E:144 , PHE E:270 , LYS E:280
BINDING SITE FOR RESIDUE EDO A 3
15
BC8
SOFTWARE
HIS D:150 , ARG D:284 , HOH D:323 , HOH D:460
BINDING SITE FOR RESIDUE EDO D 4
16
BC9
SOFTWARE
HIS E:150 , ARG E:284 , HOH E:365 , HOH E:390
BINDING SITE FOR RESIDUE EDO E 5
17
CC1
SOFTWARE
HIS A:150 , ARG A:284
BINDING SITE FOR RESIDUE EDO A 9
[
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]
SAPs(SNPs)/Variants
(1, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_VP1_SV40_001 (I98L, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_VP1_SV40_001
*
I
99
L
VP1_SV40
---
---
A/B/C/D/E
I
98
L
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
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
(1, 5)
Info
All SCOP Domains
1a: SCOP_d3bwra_ (A:)
1b: SCOP_d3bwrb_ (B:)
1c: SCOP_d3bwrc_ (C:)
1d: SCOP_d3bwrd_ (D:)
1e: SCOP_d3bwre_ (E:)
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Protein Domains
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(
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Organisms
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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)
Simian virus 40 [TaxId: 10633]
(2)
1a
d3bwra_
A:
1b
d3bwrb_
B:
1c
d3bwrc_
C:
1d
d3bwrd_
D:
1e
d3bwre_
E:
[
close SCOP info
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_3bwrA00 (A:31-297)
1b: CATH_3bwrC00 (C:31-297)
1c: CATH_3bwrD00 (D:31-297)
1d: CATH_3bwrE00 (E:32-297)
1e: CATH_3bwrB00 (B:43-297)
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Topologies
(
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(
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Polyomavirus Vp1; Chain A
(9)
Homologous Superfamily
:
Polyomavirus Vp1, chain A
(8)
Simian virus 40. Organism_taxid: 10633.
(2)
1a
3bwrA00
A:31-297
1b
3bwrC00
C:31-297
1c
3bwrD00
D:31-297
1d
3bwrE00
E:32-297
1e
3bwrB00
B:43-297
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain D
Chain E
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Asym.Unit (235 KB)
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