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4MJ0
Asym. Unit
Info
Asym.Unit (485 KB)
Biol.Unit 1 (473 KB)
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(1)
Title
:
BK POLYOMAVIRUS VP1 PENTAMER IN COMPLEX WITH GD3 OLIGOSACCHARIDE
Authors
:
U. Neu, L. J. Stroh, T. Stehle
Date
:
03 Sep 13 (Deposition) - 06 Nov 13 (Release) - 06 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Antiparallel Beta Sandwich, Jelly-Roll Topology, Viral Protein, Polyomavirus, Receptor-Switching, Glycan Receptor, Virus Major Capsid Protein, Attachment To Host-Cell Surface Receptors
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Neu, S. A. Allen, B. S. Blaum, Y. Liu, M. Frank, A. S. Palma, L. J. Stroh T. Feizi, T. Peters, W. J. Atwood, T. Stehle
A Structure-Guided Mutation In The Major Capsid Protein Retargets Bk Polyomavirus.
Plos Pathog. V. 9 03688 2013
[
close entry info
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Hetero Components
(5, 23)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
4g: GLYCEROL (GOLg)
5a: O-SIALIC ACID (SIAa)
5b: O-SIALIC ACID (SIAb)
5c: O-SIALIC ACID (SIAc)
5d: O-SIALIC ACID (SIAd)
5e: O-SIALIC ACID (SIAe)
5f: O-SIALIC ACID (SIAf)
5g: O-SIALIC ACID (SIAg)
5h: O-SIALIC ACID (SIAh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
2
CL
5
Ligand/Ion
CHLORIDE ION
3
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
7
Ligand/Ion
GLYCEROL
5
SIA
8
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
LEU A:62 , LEU A:67 , LYS A:68 , ASN A:272 , SER A:274 , THR A:276 , GLN A:278 , SIA A:402 , HOH A:574 , HOH A:596 , HOH A:619 , HOH A:684 , HOH A:697 , HOH B:590
BINDING SITE FOR RESIDUE SIA A 401
02
AC2
SOFTWARE
HIS A:150 , GLY A:222 , THR A:223 , HOH A:632 , HOH A:800
BINDING SITE FOR RESIDUE GOL A 405
03
AC3
SOFTWARE
LYS A:180 , HIS A:193 , HOH A:795
BINDING SITE FOR RESIDUE CL A 406
04
AC4
SOFTWARE
LEU B:62 , LEU B:67 , LYS B:68 , ASN B:272 , SER B:274 , THR B:276 , GLN B:278 , SIA B:402 , HOH B:542 , HOH B:548 , HOH B:640 , HOH B:677 , HOH B:723 , HOH C:540
BINDING SITE FOR RESIDUE SIA B 401
05
AC5
SOFTWARE
HIS A:138 , LYS B:68 , THR B:276 , SIA B:401
BINDING SITE FOR RESIDUE SIA B 402
06
AC6
SOFTWARE
GLU B:216 , ASN B:217 , ARG B:219 , ASP B:246 , VAL B:250 , GLY B:251 , PRO B:252 , HOH B:585 , HOH B:703
BINDING SITE FOR RESIDUE GOL B 403
07
AC7
SOFTWARE
HIS B:150 , PHE B:221 , GLY B:222 , THR B:223 , HOH B:570
BINDING SITE FOR RESIDUE GOL B 404
08
AC8
SOFTWARE
LYS B:180 , HIS B:193
BINDING SITE FOR RESIDUE CL B 405
09
AC9
SOFTWARE
LEU C:62 , LEU C:67 , LYS C:68 , ASN C:272 , SER C:274 , THR C:276 , GLN C:278 , SIA C:402 , HOH C:534 , HOH C:554 , HOH C:585 , HOH C:638 , HOH C:662 , HOH D:593
BINDING SITE FOR RESIDUE SIA C 401
10
BC1
SOFTWARE
HIS C:150 , PHE C:221 , GLY C:222 , THR C:223 , HOH C:536
BINDING SITE FOR RESIDUE GOL C 404
11
BC2
SOFTWARE
LYS C:180 , HIS C:193
BINDING SITE FOR RESIDUE CL C 405
12
BC3
SOFTWARE
LEU D:62 , LEU D:67 , LYS D:68 , ASN D:272 , SER D:274 , THR D:276 , GLN D:278 , SIA D:402 , HOH D:525 , HOH D:527 , HOH D:541 , HOH D:602 , HOH D:603 , HOH D:625 , HOH D:641
BINDING SITE FOR RESIDUE SIA D 401
13
BC4
SOFTWARE
GLY D:40 , ASP D:59 , SIA D:401 , HOH D:527 , HOH D:625 , HOH D:745 , HOH D:755 , HOH E:591
BINDING SITE FOR RESIDUE SIA D 402
14
BC5
SOFTWARE
HIS D:150 , PHE D:221 , GLY D:222 , THR D:223 , HOH D:709
BINDING SITE FOR RESIDUE GOL D 403
15
BC6
SOFTWARE
LYS D:180 , HIS D:193
BINDING SITE FOR RESIDUE CL D 404
16
BC7
SOFTWARE
GLU E:216 , ASN E:217 , ARG E:219 , ASP E:246 , VAL E:250 , GLY E:251 , PRO E:252
BINDING SITE FOR RESIDUE GOL E 401
17
BC8
SOFTWARE
HIS E:150 , PHE E:221 , GLY E:222 , THR E:223 , HOH E:556 , HOH E:769
BINDING SITE FOR RESIDUE GOL E 402
18
BC9
SOFTWARE
LYS E:180 , HIS E:193
BINDING SITE FOR RESIDUE CL E 403
19
CC1
SOFTWARE
VAL A:34 , LEU A:35 , GLU A:36 , VAL A:37 , THR A:39 , LYS A:68 , GLY A:249 , ARG A:293 , SIA A:401 , HOH A:566 , HOH A:627 , HOH A:655 , HOH A:702 , HOH A:729 , HOH A:747 , HOH A:775 , ASP B:74 , HIS E:138
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 402 TO 404
20
CC2
SOFTWARE
HIS B:138 , LYS C:68 , THR C:276 , SIA C:401 , HOH C:662 , HOH C:669
BINDING SITE FOR CHAIN C OF RESIDUES SIA C 402 AND GAL C 403
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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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
(1, 5)
Info
All SCOP Domains
1a: SCOP_d4mj0a_ (A:)
1b: SCOP_d4mj0b_ (B:)
1c: SCOP_d4mj0c_ (C:)
1d: SCOP_d4mj0d_ (D:)
1e: SCOP_d4mj0e_ (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
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Bk polyomavirus [TaxId: 10629]
(2)
1a
d4mj0a_
A:
1b
d4mj0b_
B:
1c
d4mj0c_
C:
1d
d4mj0d_
D:
1e
d4mj0e_
E:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (485 KB)
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