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4POS
Biol. Unit 1
Info
Asym.Unit (919 KB)
Biol.Unit 1 (453 KB)
Biol.Unit 2 (456 KB)
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(1)
Title
:
STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WITH 3'-SIALYLLACTOSAMINE
Authors
:
Z. M. Khan, T. Stehle
Date
:
26 Feb 14 (Deposition) - 09 Apr 14 (Release) - 26 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Jelly Roll Fold, Capsid Formation, Receptor Interaction, Carbohydrate, Sialyloligosaccharide, Viral Coat Protein, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. M. Khan, Y. Liu, U. Neu, M. Gilbert, B. Ehlers, T. Feizi, T. Stehle
Crystallographic And Glycan Microarray Analysis Of Human Polyomavirus 9 Vp1 Identifies N-Glycolyl Neuraminic Acid As A Receptor Candidate.
J. Virol. V. 88 6100 2014
[
close entry info
]
Hetero Components
(5, 32)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
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)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
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)
3g: BETA-D-GALACTOSE (GALg)
3h: BETA-D-GALACTOSE (GALh)
3i: BETA-D-GALACTOSE (GALi)
4a: ISOPROPYL ALCOHOL (IPAa)
4b: ISOPROPYL ALCOHOL (IPAb)
4c: ISOPROPYL ALCOHOL (IPAc)
4d: ISOPROPYL ALCOHOL (IPAd)
4e: ISOPROPYL ALCOHOL (IPAe)
4f: ISOPROPYL ALCOHOL (IPAf)
4g: ISOPROPYL ALCOHOL (IPAg)
4h: ISOPROPYL ALCOHOL (IPAh)
4i: ISOPROPYL ALCOHOL (IPAi)
4j: ISOPROPYL ALCOHOL (IPAj)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6a: O-SIALIC ACID (SIAa)
6b: O-SIALIC ACID (SIAb)
6c: O-SIALIC ACID (SIAc)
6d: O-SIALIC ACID (SIAd)
6e: O-SIALIC ACID (SIAe)
6f: O-SIALIC ACID (SIAf)
6g: O-SIALIC ACID (SIAg)
6h: O-SIALIC ACID (SIAh)
6i: O-SIALIC ACID (SIAi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
4
IPA
5
Ligand/Ion
ISOPROPYL ALCOHOL
5
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SIA
4
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(31, 31)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: FC6 (SOFTWARE)
27: FC7 (SOFTWARE)
28: FC8 (SOFTWARE)
29: FC9 (SOFTWARE)
30: GC3 (SOFTWARE)
31: GC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:49 , HOH A:589 , HOH A:678 , SER B:217 , HOH B:646
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
LYS A:198 , SER A:217 , TYR E:51 , MET E:123
BINDING SITE FOR RESIDUE EDO A 402
03
AC3
SOFTWARE
GLY A:134 , GLY A:135 , TYR A:137 , TYR A:277 , HOH A:712 , ALA B:75 , SER B:76
BINDING SITE FOR RESIDUE EDO A 403
04
AC4
SOFTWARE
GLU A:220 , ASN A:221 , ARG A:223 , ASP A:250 , VAL A:254 , GLY A:255
BINDING SITE FOR RESIDUE EDO A 404
05
AC5
SOFTWARE
SER A:77 , ALA A:79 , NAG E:406 , HOH E:546 , ILE H:48 , GLU H:49 , ILE H:96 , HOH H:763
BINDING SITE FOR RESIDUE EDO A 405
06
AC6
SOFTWARE
ARG A:223 , LEU A:249 , ASP A:250 , HOH A:687 , HOH A:724 , LYS E:119 , ASN E:242 , SER E:243
BINDING SITE FOR RESIDUE EDO A 406
07
AC7
SOFTWARE
VAL A:122 , HIS A:154 , MET A:238 , GLN A:239 , HOH A:611 , HOH A:652
BINDING SITE FOR RESIDUE EDO A 407
08
AC8
SOFTWARE
HIS A:154 , PHE A:156 , TYR A:225 , SER A:227 , HOH A:652
BINDING SITE FOR RESIDUE IPA A 408
09
AC9
SOFTWARE
GLU B:49 , SER C:217 , HOH C:697 , HOH C:711
BINDING SITE FOR RESIDUE CA B 401
10
BC1
SOFTWARE
TYR A:51 , MET A:123 , LYS B:198 , SER B:217 , HOH B:743
BINDING SITE FOR RESIDUE EDO B 402
11
BC2
SOFTWARE
TYR B:51 , MET B:123 , HOH B:711 , LYS C:198 , SER C:217
BINDING SITE FOR RESIDUE EDO B 403
12
BC3
SOFTWARE
ASN A:242 , SER A:243 , ARG B:223 , LEU B:249 , ASP B:250
BINDING SITE FOR RESIDUE EDO B 404
13
BC4
SOFTWARE
THR B:246 , IPA B:406 , HOH B:661
BINDING SITE FOR RESIDUE EDO B 405
14
BC5
SOFTWARE
HIS B:154 , TYR B:225 , GLY B:226 , SER B:227 , EDO B:405 , HOH B:512
BINDING SITE FOR RESIDUE IPA B 406
15
BC6
SOFTWARE
GLU C:49 , HOH C:693 , SER D:217 , HOH D:501 , HOH D:667
BINDING SITE FOR RESIDUE CA C 401
16
BC7
SOFTWARE
TYR C:68 , HIS C:274 , ASN C:276 , ASN C:282
BINDING SITE FOR RESIDUE EDO C 402
17
BC8
SOFTWARE
HIS C:154 , PHE C:156 , TYR C:225 , GLY C:226 , SER C:227 , HOH C:623
BINDING SITE FOR RESIDUE IPA C 403
18
BC9
SOFTWARE
GLU D:49 , SER E:217 , HOH E:702
BINDING SITE FOR RESIDUE CA D 401
19
CC1
SOFTWARE
GLY D:134 , GLY D:135 , TYR D:137 , HOH D:691 , ALA E:75 , SER E:76
BINDING SITE FOR RESIDUE EDO D 402
20
CC2
SOFTWARE
GLU D:220 , ASN D:221 , ASP D:250 , VAL D:254 , GLY D:255 , PRO D:256
BINDING SITE FOR RESIDUE EDO D 403
21
CC3
SOFTWARE
HIS D:154 , PHE D:156 , TYR D:225 , SER D:227 , HOH D:584
BINDING SITE FOR RESIDUE IPA D 404
22
CC4
SOFTWARE
SER A:217 , GLU A:220 , HOH A:704 , GLU E:49 , HOH E:501 , HOH E:729
BINDING SITE FOR RESIDUE CA E 401
23
CC5
SOFTWARE
TYR D:51 , GLN E:166 , LYS E:198 , SER E:217
BINDING SITE FOR RESIDUE EDO E 402
24
CC6
SOFTWARE
TYR E:225 , THR E:246 , IPA E:404
BINDING SITE FOR RESIDUE EDO E 403
25
CC7
SOFTWARE
HIS E:154 , PHE E:156 , TYR E:225 , SER E:227 , EDO E:403 , HOH E:623
BINDING SITE FOR RESIDUE IPA E 404
26
FC6
SOFTWARE
LEU A:65 , TYR A:68 , ASP A:71 , GLN A:133 , GLY A:134 , HIS A:274 , ASN A:276 , TYR A:277 , ASN A:282 , HOH A:569 , HOH A:570 , HOH A:610 , HOH A:647 , HOH A:712 , HOH A:713 , HOH A:714 , SER B:76 , SER B:77 , LYS B:78
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 409 TO 411
27
FC7
SOFTWARE
LEU B:65 , TYR B:68 , ASP B:71 , GLN B:133 , GLY B:134 , HIS B:274 , ASN B:276 , TYR B:277 , ASN B:282 , HOH B:525 , HOH B:553 , HOH B:560 , HOH B:575 , HOH B:601 , HOH B:648 , HOH B:658 , HOH B:665 , HOH B:739 , HOH B:740 , HOH B:752 , HOH B:753 , HOH B:754 , SER C:76 , SER C:77 , LYS C:78 , HOH C:567
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 407 TO 409
28
FC8
SOFTWARE
LEU D:65 , TYR D:68 , ASP D:71 , GLN D:133 , GLY D:134 , HIS D:274 , ASN D:276 , TYR D:277 , ASN D:282 , HOH D:601 , HOH D:653 , HOH D:673 , HOH D:691 , HOH D:719 , HOH D:720 , HOH D:727 , HOH D:737 , SER E:76 , SER E:77 , LYS E:78 , HOH E:616 , ASN G:102 , MET G:105 , LEU G:110 , ASN G:301 , HOH G:730
BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 405 TO 407
29
FC9
SOFTWARE
SER A:77 , LYS A:78 , EDO A:405 , HOH A:715 , LEU E:65 , TYR E:68 , ASP E:71 , GLN E:133 , GLY E:134 , HIS E:274 , ASN E:276 , TYR E:277 , ASN E:282 , HOH E:546 , HOH E:551 , HOH E:556 , HOH E:557 , HOH E:565 , HOH E:632 , HOH E:656 , HOH E:695 , HOH E:708 , HOH E:727 , HOH E:741 , HOH E:746 , HOH E:753 , GLU H:49 , HOH I:687
BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 405 TO 407
30
GC3
SOFTWARE
HOH C:629 , LEU H:65 , TYR H:68 , ASP H:71 , GLN H:133 , GLY H:134 , HIS H:274 , ASN H:276 , TYR H:277 , ASN H:282 , HOH H:512 , HOH H:525 , HOH H:535 , HOH H:581 , HOH H:606 , HOH H:616 , HOH H:625 , HOH H:641 , HOH H:669 , HOH H:682 , HOH H:738 , HOH H:767 , SER I:76 , SER I:77 , LYS I:78
BINDING SITE FOR CHAIN H OF POLYSACCHARIDE RESIDUES 407 TO 409
31
GC5
SOFTWARE
MET B:100 , GLU B:103 , HOH B:626 , SER F:76 , SER F:77 , LYS F:78 , ASP H:108 , LEU J:65 , TYR J:68 , ASP J:71 , GLN J:133 , GLY J:134 , HIS J:274 , ASN J:276 , TYR J:277 , ASN J:282 , HOH J:535 , HOH J:541 , HOH J:542 , HOH J:552 , HOH J:586 , HOH J:591 , HOH J:598 , HOH J:615 , HOH J:623 , HOH J:668 , HOH J:718 , HOH J:754 , HOH J:756
BINDING SITE FOR CHAIN J OF POLYSACCHARIDE RESIDUES 404 TO 406
[
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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
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Exons
(0, 0)
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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, 10)
Info
All SCOP Domains
1a: SCOP_d4posa_ (A:)
1b: SCOP_d4posb_ (B:)
1c: SCOP_d4posc_ (C:)
1d: SCOP_d4posd_ (D:)
1e: SCOP_d4pose_ (E:)
1f: SCOP_d4posf_ (F:)
1g: SCOP_d4posg_ (G:)
1h: SCOP_d4posh_ (H:)
1i: SCOP_d4posi_ (I:)
1j: SCOP_d4posj_ (J:)
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Protein Domains
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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
:
Papovaviridae-like VP
(19)
Protein domain
:
automated matches
(12)
Human polyomavirus 9 [TaxId: 943908]
(7)
1a
d4posa_
A:
1b
d4posb_
B:
1c
d4posc_
C:
1d
d4posd_
D:
1e
d4pose_
E:
1f
d4posf_
F:
1g
d4posg_
G:
1h
d4posh_
H:
1i
d4posi_
I:
1j
d4posj_
J:
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CATH Domains
(0, 0)
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Pfam Domains
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