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1VPS
Biol. Unit 1
Info
Asym.Unit (282 KB)
Biol.Unit 1 (275 KB)
Biol.Unit 2 (545 KB)
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(1)
Title
:
POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE
Authors
:
T. Stehle, S. C. Harrison
Date
:
07 Mar 97 (Deposition) - 15 May 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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
:
Virus Coat Protein, Oligosaccharide Binding, Virus Assembly, Sialic Acid, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Stehle, S. C. Harrison
High-Resolution Structure Of A Polyomavirus Vp1-Oligosaccharide Complex: Implications For Assembly And Receptor Binding.
Embo J. V. 16 5139 1997
(for further references see the
PDB file header
)
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: BETA-D-GALACTOSE (GALa)
1b: BETA-D-GALACTOSE (GALb)
1c: BETA-D-GALACTOSE (GALc)
1d: BETA-D-GALACTOSE (GALd)
1e: BETA-D-GALACTOSE (GALe)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3a: O-SIALIC ACID (SIAa)
3b: O-SIALIC ACID (SIAb)
3c: O-SIALIC ACID (SIAc)
3d: O-SIALIC ACID (SIAd)
3e: O-SIALIC ACID (SIAe)
3f: O-SIALIC ACID (SIAf)
3g: O-SIALIC ACID (SIAg)
3h: O-SIALIC ACID (SIAh)
3i: O-SIALIC ACID (SIAi)
3j: O-SIALIC ACID (SIAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GAL
5
Ligand/Ion
BETA-D-GALACTOSE
2
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
SIA
10
Ligand/Ion
O-SIALIC ACID
[
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Sites
(20, 20)
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)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GAL A:2 , TYR A:72 , ARG A:77 , GLY A:78 , THR A:291 , ASN A:293 , HIS A:298 , HOH A:496 , HOH A:499 , HOH A:603 , HOH A:662 , HOH A:669 , HOH A:678 , ASP B:85
BINDING SITE FOR RESIDUE SIA A 1
02
AC2
SOFTWARE
SIA A:1 , NAG A:3 , GLY A:78 , ASN A:93 , THR A:94 , HOH A:660 , HOH A:662 , HOH A:663
BINDING SITE FOR RESIDUE GAL A 2
03
AC3
SOFTWARE
GAL A:2 , SIA A:4
BINDING SITE FOR RESIDUE NAG A 3
04
AC4
SOFTWARE
NAG A:3 , ASN A:80 , LEU A:81 , THR A:83 , SER A:89 , LYS A:186 , HOH A:400 , HOH A:414 , HOH A:698
BINDING SITE FOR RESIDUE SIA A 4
05
AC5
SOFTWARE
GAL B:2 , TYR B:72 , ARG B:77 , GLY B:78 , THR B:291 , ASN B:293 , HIS B:298 , HOH B:518 , HOH B:521 , HOH B:570 , HOH B:714 , HOH B:715 , HOH B:725 , ASP C:85
BINDING SITE FOR RESIDUE SIA B 1
06
AC6
SOFTWARE
SIA B:1 , NAG B:3 , GLY B:78 , ASN B:93 , THR B:94 , HOH B:659 , HOH B:684 , HOH B:713 , HOH B:714
BINDING SITE FOR RESIDUE GAL B 2
07
AC7
SOFTWARE
GAL B:2 , SIA B:4 , HOH B:713
BINDING SITE FOR RESIDUE NAG B 3
08
AC8
SOFTWARE
NAG B:3 , ASN B:80 , LEU B:81 , THR B:83 , SER B:89 , LYS B:186 , HOH B:434 , HOH B:711 , HOH B:712
BINDING SITE FOR RESIDUE SIA B 4
09
AC9
SOFTWARE
GAL C:2 , TYR C:72 , ARG C:77 , GLY C:78 , THR C:291 , ASN C:293 , HIS C:298 , HOH C:512 , HOH C:515 , HOH C:579 , HOH C:724 , HOH C:747 , HOH C:758 , ASP D:85
BINDING SITE FOR RESIDUE SIA C 1
10
BC1
SOFTWARE
SIA C:1 , NAG C:3 , GLY C:78 , ASN C:93 , THR C:94 , HOH C:598 , HOH C:626 , HOH C:724 , HOH C:726
BINDING SITE FOR RESIDUE GAL C 2
11
BC2
SOFTWARE
GAL C:2 , SIA C:4 , HOH C:598
BINDING SITE FOR RESIDUE NAG C 3
12
BC3
SOFTWARE
NAG C:3 , ASN C:80 , LEU C:81 , SER C:89 , HOH C:418 , HOH C:432 , HOH C:749
BINDING SITE FOR RESIDUE SIA C 4
13
BC4
SOFTWARE
GAL D:2 , TYR D:72 , ARG D:77 , GLY D:78 , THR D:291 , ASN D:293 , HIS D:298 , HOH D:523 , HOH D:526 , HOH D:634 , HOH D:719 , HOH D:720 , HOH D:735 , HOH D:742 , HOH D:749 , ASP E:85
BINDING SITE FOR RESIDUE SIA D 1
14
BC5
SOFTWARE
SIA D:1 , NAG D:3 , GLY D:78 , ASN D:93 , THR D:94 , HOH D:717 , HOH D:720 , HOH D:726
BINDING SITE FOR RESIDUE GAL D 2
15
BC6
SOFTWARE
TYR C:294 , GAL D:2 , SIA D:4 , HOH D:734 , HOH D:740
BINDING SITE FOR RESIDUE NAG D 3
16
BC7
SOFTWARE
ASN B:149 , HOH B:650 , TYR C:294 , NAG D:3 , ASN D:80 , LEU D:81 , THR D:83 , SER D:89 , LYS D:186 , HOH D:628 , HOH D:718 , HOH D:728
BINDING SITE FOR RESIDUE SIA D 4
17
BC8
SOFTWARE
ASP A:85 , GAL E:2 , TYR E:72 , ARG E:77 , GLY E:78 , THR E:291 , ASN E:293 , HIS E:298 , HOH E:528 , HOH E:531 , HOH E:595 , HOH E:668 , HOH E:672
BINDING SITE FOR RESIDUE SIA E 1
18
BC9
SOFTWARE
SIA E:1 , NAG E:3 , GLY E:78 , ASN E:93 , THR E:94 , HOH E:668 , HOH E:670
BINDING SITE FOR RESIDUE GAL E 2
19
CC1
SOFTWARE
GAL E:2 , SIA E:4 , HOH E:698
BINDING SITE FOR RESIDUE NAG E 3
20
CC2
SOFTWARE
NAG E:3 , ASN E:80 , LEU E:81 , THR E:83 , SER E:89 , HOH E:435 , HOH E:665
BINDING SITE FOR RESIDUE SIA E 4
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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_d1vpsa_ (A:)
1b: SCOP_d1vpsb_ (B:)
1c: SCOP_d1vpsc_ (C:)
1d: SCOP_d1vpsd_ (D:)
1e: SCOP_d1vpse_ (E:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
Group I dsDNA viruses
(30)
Family
:
Papovaviridae-like VP
(19)
Protein domain
:
Polyomavirus coat proteins
(6)
Murine polyomavirus, strain small-plaque 16 [TaxId: 10634]
(5)
1a
d1vpsa_
A:
1b
d1vpsb_
B:
1c
d1vpsc_
C:
1d
d1vpsd_
D:
1e
d1vpse_
E:
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1vpsB00 (B:32-320)
1b: CATH_1vpsA00 (A:32-316)
1c: CATH_1vpsC00 (C:32-316)
1d: CATH_1vpsD00 (D:32-316)
1e: CATH_1vpsE00 (E:32-316)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Polyomavirus Vp1; Chain A
(9)
Homologous Superfamily
:
Polyomavirus Vp1, chain A
(8)
Murine polyomavirus. Organism_taxid: 10634.
(2)
1a
1vpsB00
B:32-320
1b
1vpsA00
A:32-316
1c
1vpsC00
C:32-316
1d
1vpsD00
D:32-316
1e
1vpsE00
E:32-316
[
close CATH info
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Polyoma_coat_1vpsE01 (E:32-316)
1b: PFAM_Polyoma_coat_1vpsE02 (E:32-316)
1c: PFAM_Polyoma_coat_1vpsE03 (E:32-316)
1d: PFAM_Polyoma_coat_1vpsE04 (E:32-316)
1e: PFAM_Polyoma_coat_1vpsE05 (E:32-316)
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Organisms
(
)
(
)
Clan
:
no clan defined [family: Polyoma_coat]
(8)
Family
:
Polyoma_coat
(8)
Murine polyomavirus (strain P16 small-plaque) (MPyV)
(4)
1a
Polyoma_coat-1vpsE01
E:32-316
1b
Polyoma_coat-1vpsE02
E:32-316
1c
Polyoma_coat-1vpsE03
E:32-316
1d
Polyoma_coat-1vpsE04
E:32-316
1e
Polyoma_coat-1vpsE05
E:32-316
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