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4POR
Biol. Unit 1
Info
Asym.Unit (916 KB)
Biol.Unit 1 (453 KB)
Biol.Unit 2 (454 KB)
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(1)
Title
:
STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WITH 3'-SIALYLLACTOSE
Authors
:
Z. M. Khan, T. Stehle
Date
:
26 Feb 14 (Deposition) - 09 Apr 14 (Release) - 26 Nov 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.09
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, 35)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
1e: BETA-D-GLUCOSE (BGCe)
1f: BETA-D-GLUCOSE (BGCf)
1g: BETA-D-GLUCOSE (BGCg)
1h: BETA-D-GLUCOSE (BGCh)
1i: BETA-D-GLUCOSE (BGCi)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3ag: 1,2-ETHANEDIOL (EDOag)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: BETA-D-GALACTOSE (GALa)
4b: BETA-D-GALACTOSE (GALb)
4c: BETA-D-GALACTOSE (GALc)
4d: BETA-D-GALACTOSE (GALd)
4e: BETA-D-GALACTOSE (GALe)
4f: BETA-D-GALACTOSE (GALf)
4g: BETA-D-GALACTOSE (GALg)
4h: BETA-D-GALACTOSE (GALh)
4i: BETA-D-GALACTOSE (GALi)
5a: ISOPROPYL ALCOHOL (IPAa)
5b: ISOPROPYL ALCOHOL (IPAb)
5c: ISOPROPYL ALCOHOL (IPAc)
5d: ISOPROPYL ALCOHOL (IPAd)
5e: ISOPROPYL ALCOHOL (IPAe)
5f: ISOPROPYL ALCOHOL (IPAf)
5g: ISOPROPYL ALCOHOL (IPAg)
5h: ISOPROPYL ALCOHOL (IPAh)
5i: ISOPROPYL ALCOHOL (IPAi)
5j: ISOPROPYL ALCOHOL (IPAj)
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
BGC
4
Ligand/Ion
BETA-D-GLUCOSE
2
CA
-1
Ligand/Ion
CALCIUM ION
3
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
4
GAL
4
Ligand/Ion
BETA-D-GALACTOSE
5
IPA
5
Ligand/Ion
ISOPROPYL ALCOHOL
6
SIA
4
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(34, 34)
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: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: EC8 (SOFTWARE)
30: FC9 (SOFTWARE)
31: GC1 (SOFTWARE)
32: GC2 (SOFTWARE)
33: GC3 (SOFTWARE)
34: GC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:49 , HOH A:670 , SER B:217 , HOH B:506
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
VAL A:122 , HIS A:154 , MET A:238 , GLN A:239 , HOH A:582 , HOH A:689
BINDING SITE FOR RESIDUE EDO A 402
03
AC3
SOFTWARE
GLY A:134 , GLY A:135 , TYR A:137 , HOH A:598 , ALA B:75 , SER B:76
BINDING SITE FOR RESIDUE EDO A 403
04
AC4
SOFTWARE
LYS A:198 , SER A:217 , HOH A:663 , TYR E:51 , MET E:123 , TYR E:289
BINDING SITE FOR RESIDUE EDO A 404
05
AC5
SOFTWARE
PHE A:156 , TYR A:225 , SER A:227 , HOH A:689
BINDING SITE FOR RESIDUE IPA A 405
06
AC6
SOFTWARE
GLU B:49 , SER C:217 , GLU C:220 , HOH C:696
BINDING SITE FOR RESIDUE CA B 401
07
AC7
SOFTWARE
HIS B:154 , MET B:238 , GLN B:239 , HOH B:673 , HOH B:682
BINDING SITE FOR RESIDUE EDO B 402
08
AC8
SOFTWARE
TYR A:51 , LYS B:198 , SER B:217 , HOH B:720
BINDING SITE FOR RESIDUE EDO B 403
09
AC9
SOFTWARE
SER A:243 , HOH A:703 , ARG B:223 , TYR B:225 , VAL B:247 , LEU B:248 , LEU B:249 , ASP B:250 , HOH B:557 , HOH B:603
BINDING SITE FOR RESIDUE EDO B 404
10
BC1
SOFTWARE
HIS B:154 , PHE B:156 , TYR B:225 , GLY B:226 , SER B:227 , HOH B:682
BINDING SITE FOR RESIDUE IPA B 405
11
BC2
SOFTWARE
GLU C:49 , SER D:217 , HOH D:509
BINDING SITE FOR RESIDUE CA C 401
12
BC3
SOFTWARE
MET C:238 , GLN C:239 , HOH C:559 , HOH C:618 , HOH C:697
BINDING SITE FOR RESIDUE EDO C 402
13
BC4
SOFTWARE
TYR B:51 , GLN C:166 , LYS C:198 , SER C:217 , HOH C:654 , HOH C:701
BINDING SITE FOR RESIDUE EDO C 403
14
BC5
SOFTWARE
GLY C:134 , GLY C:135 , TYR C:137 , TYR C:277 , HOH C:700 , VAL D:74 , ALA D:75
BINDING SITE FOR RESIDUE EDO C 404
15
BC6
SOFTWARE
GLY B:134 , GLY B:135 , TYR B:137 , TYR B:277 , HOH B:690 , ALA C:75 , SER C:76
BINDING SITE FOR RESIDUE EDO C 405
16
BC7
SOFTWARE
HIS C:154 , PHE C:156 , TYR C:225 , SER C:227
BINDING SITE FOR RESIDUE IPA C 406
17
BC8
SOFTWARE
GLU D:49 , SER E:217 , HOH E:604
BINDING SITE FOR RESIDUE CA D 401
18
BC9
SOFTWARE
MET D:238 , GLN D:239 , HOH D:644 , HOH D:685
BINDING SITE FOR RESIDUE EDO D 402
19
CC1
SOFTWARE
TYR C:51 , LYS D:198 , SER D:217
BINDING SITE FOR RESIDUE EDO D 403
20
CC2
SOFTWARE
LYS C:119 , ASN C:242 , ARG D:223 , VAL D:247 , LEU D:249 , ASP D:250 , HOH D:524 , HOH D:699
BINDING SITE FOR RESIDUE EDO D 404
21
CC3
SOFTWARE
GLY D:134 , GLY D:135 , TYR D:137 , HOH D:678 , ALA E:75 , SER E:76
BINDING SITE FOR RESIDUE EDO D 405
22
CC4
SOFTWARE
HIS D:154 , PHE D:156 , TYR D:225 , GLY D:226 , SER D:227 , HOH D:644
BINDING SITE FOR RESIDUE IPA D 406
23
CC5
SOFTWARE
SER A:217 , HOH A:508 , HOH A:668 , GLU E:49
BINDING SITE FOR RESIDUE CA E 401
24
CC6
SOFTWARE
VAL E:122 , HIS E:154 , MET E:238 , GLN E:239 , HOH E:519 , HOH E:524
BINDING SITE FOR RESIDUE EDO E 402
25
CC7
SOFTWARE
ALA A:75 , SER A:76 , GLY E:134 , GLY E:135 , TYR E:137 , TYR E:277
BINDING SITE FOR RESIDUE EDO E 403
26
CC8
SOFTWARE
TYR D:51 , MET D:123 , LYS E:198 , SER E:217
BINDING SITE FOR RESIDUE EDO E 404
27
CC9
SOFTWARE
ASN E:53 , ARG E:55 , HOH E:708
BINDING SITE FOR RESIDUE EDO E 405
28
DC1
SOFTWARE
PHE E:156 , TYR E:225 , SER E:227
BINDING SITE FOR RESIDUE IPA E 406
29
EC8
SOFTWARE
THR B:109 , HOH B:567 , ARG H:39 , THR H:109
BINDING SITE FOR RESIDUE EDO H 405
30
FC9
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:535 , HOH A:544 , HOH A:595 , HOH A:598 , HOH A:612 , HOH A:614 , HOH A:648 , HOH A:674 , HOH A:697 , HOH A:714 , HOH A:741 , HOH A:747 , SER B:76 , SER B:77 , LYS B:78
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 406 TO 408
31
GC1
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:529 , HOH B:530 , HOH B:532 , HOH B:591 , HOH B:604 , HOH B:605 , HOH B:636 , HOH B:638 , HOH B:688 , HOH B:690 , HOH B:712 , HOH B:742 , HOH B:752 , SER C:76 , SER C:77 , LYS C:78 , HOH C:512
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 406 TO 408
32
GC2
SOFTWARE
LEU D:65 , TYR D:68 , ASP D:71 , GLN D:133 , GLY D:134 , GLY D:135 , HIS D:274 , ASN D:276 , TYR D:277 , ASN D:282 , HOH D:518 , HOH D:564 , HOH D:577 , HOH D:677 , HOH D:678 , HOH D:686 , SER E:76 , SER E:77 , LYS E:78 , MET G:100 , ASN G:102 , LEU G:110
BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 407 TO 409
33
GC3
SOFTWARE
SER A:76 , SER A:77 , LYS A:78 , HOH A:503 , 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:513 , HOH E:543 , HOH E:548 , HOH E:561 , HOH E:566 , HOH E:567 , HOH E:584 , HOH E:663 , HOH E:668 , HOH E:702 , HOH H:589 , HOH H:745 , HOH H:746
BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 407 TO 409
34
GC6
SOFTWARE
HOH C:657 , LEU H:65 , TYR H:68 , ASP H:71 , GLN H:133 , GLY H:134 , HIS H:274 , ASN H:276 , TYR H:277 , HOH H:504 , HOH H:564 , HOH H:567 , HOH H:571 , HOH H:572 , HOH H:583 , HOH H:606 , HOH H:610 , HOH H:687 , HOH H:689 , SER I:76 , SER I:77 , LYS I:78 , HOH I:504
BINDING SITE FOR CHAIN H OF POLYSACCHARIDE RESIDUES 407 TO 409
[
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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)
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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, 10)
Info
All SCOP Domains
1a: SCOP_d4pora_ (A:)
1b: SCOP_d4porb_ (B:)
1c: SCOP_d4porc_ (C:)
1d: SCOP_d4pord_ (D:)
1e: SCOP_d4pore_ (E:)
1f: SCOP_d4porf_ (F:)
1g: SCOP_d4porg_ (G:)
1h: SCOP_d4porh_ (H:)
1i: SCOP_d4pori_ (I:)
1j: SCOP_d4porj_ (J:)
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Protein Domains
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(
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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
:
automated matches
(12)
Human polyomavirus 9 [TaxId: 943908]
(7)
1a
d4pora_
A:
1b
d4porb_
B:
1c
d4porc_
C:
1d
d4pord_
D:
1e
d4pore_
E:
1f
d4porf_
F:
1g
d4porg_
G:
1h
d4porh_
H:
1i
d4pori_
I:
1j
d4porj_
J:
[
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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