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4POS
Biol. Unit 2
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, 35)
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
5
Ligand/Ion
BETA-D-GALACTOSE
4
IPA
5
Ligand/Ion
ISOPROPYL ALCOHOL
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
SIA
5
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(33, 33)
Info
All Sites
01: AC5 (SOFTWARE)
02: CC8 (SOFTWARE)
03: CC9 (SOFTWARE)
04: DC1 (SOFTWARE)
05: DC2 (SOFTWARE)
06: DC3 (SOFTWARE)
07: DC4 (SOFTWARE)
08: DC5 (SOFTWARE)
09: DC6 (SOFTWARE)
10: DC7 (SOFTWARE)
11: DC8 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC1 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC3 (SOFTWARE)
16: EC4 (SOFTWARE)
17: EC5 (SOFTWARE)
18: EC6 (SOFTWARE)
19: EC7 (SOFTWARE)
20: EC8 (SOFTWARE)
21: EC9 (SOFTWARE)
22: FC1 (SOFTWARE)
23: FC2 (SOFTWARE)
24: FC3 (SOFTWARE)
25: FC4 (SOFTWARE)
26: FC5 (SOFTWARE)
27: FC8 (SOFTWARE)
28: FC9 (SOFTWARE)
29: GC1 (SOFTWARE)
30: GC2 (SOFTWARE)
31: GC3 (SOFTWARE)
32: GC4 (SOFTWARE)
33: GC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
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
02
CC8
SOFTWARE
GLU F:49 , SER G:217 , HOH G:563
BINDING SITE FOR RESIDUE CA F 401
03
CC9
SOFTWARE
LYS F:198 , SER F:217 , TYR J:51 , MET J:123
BINDING SITE FOR RESIDUE EDO F 402
04
DC1
SOFTWARE
GLY F:134 , GLY F:135 , TYR F:137 , TYR F:277 , HOH F:594 , ALA G:75 , SER G:76
BINDING SITE FOR RESIDUE EDO F 403
05
DC2
SOFTWARE
GLU F:220 , ASN F:221 , THR F:222 , ARG F:223 , LEU F:248 , ASP F:250 , VAL F:254 , GLY F:255 , PRO F:256 , HOH F:755
BINDING SITE FOR RESIDUE EDO F 404
06
DC3
SOFTWARE
LYS F:119 , ASN F:242 , HOH F:768 , ARG G:223 , ASP G:250 , HOH G:635
BINDING SITE FOR RESIDUE EDO F 405
07
DC4
SOFTWARE
HIS F:154 , PHE F:156 , TYR F:225 , GLY F:226 , SER F:227 , HOH F:651
BINDING SITE FOR RESIDUE IPA F 406
08
DC5
SOFTWARE
GLU G:49 , SER H:217 , HOH H:735
BINDING SITE FOR RESIDUE CA G 401
09
DC6
SOFTWARE
TYR F:51 , TYR F:289 , LYS G:198 , SER G:217 , HOH G:729
BINDING SITE FOR RESIDUE EDO G 402
10
DC7
SOFTWARE
GLY G:134 , GLY G:135 , TYR G:137 , TYR G:277 , HOH G:675 , ALA H:75 , SER H:76
BINDING SITE FOR RESIDUE EDO G 403
11
DC8
SOFTWARE
HIS G:154 , PHE G:156 , SER G:227 , HOH G:637
BINDING SITE FOR RESIDUE IPA G 404
12
DC9
SOFTWARE
GLU H:49 , HOH H:614 , SER I:217 , GLU I:220 , HOH I:501 , HOH I:687
BINDING SITE FOR RESIDUE CA H 401
13
EC1
SOFTWARE
TYR G:51 , LYS H:198 , SER H:217
BINDING SITE FOR RESIDUE EDO H 402
14
EC2
SOFTWARE
TYR H:51 , MET H:123 , HOH H:602 , LYS I:198 , SER I:217
BINDING SITE FOR RESIDUE EDO H 403
15
EC3
SOFTWARE
GLY H:134 , GLY H:135 , TYR H:137 , TYR H:277 , HOH H:739 , ALA I:75 , SER I:76
BINDING SITE FOR RESIDUE EDO H 404
16
EC4
SOFTWARE
GLY H:57 , ASN H:59 , ASN H:60 , ASP H:63 , HOH H:548 , HOH H:621 , HOH H:751
BINDING SITE FOR RESIDUE EDO H 405
17
EC5
SOFTWARE
HIS H:154 , PHE H:156 , SER H:227 , HOH H:563
BINDING SITE FOR RESIDUE IPA H 406
18
EC6
SOFTWARE
GLU I:49 , HOH I:755 , SER J:217 , GLU J:220 , HOH J:501
BINDING SITE FOR RESIDUE CA I 401
19
EC7
SOFTWARE
TYR I:51 , MET I:123 , LYS J:198 , ASP J:215 , SER J:217
BINDING SITE FOR RESIDUE EDO I 402
20
EC8
SOFTWARE
GLU I:220 , ASN I:221 , ARG I:223 , ASP I:250 , GLY I:255 , HOH I:742 , HOH I:756
BINDING SITE FOR RESIDUE EDO I 403
21
EC9
SOFTWARE
LYS I:119 , ASN I:242 , ARG J:223 , LEU J:249 , ASP J:250
BINDING SITE FOR RESIDUE EDO I 404
22
FC1
SOFTWARE
ASN H:242 , SER H:243 , HOH H:741 , ARG I:223 , LEU I:248 , LEU I:249 , ASP I:250 , HOH I:617
BINDING SITE FOR RESIDUE EDO I 405
23
FC2
SOFTWARE
HIS I:154 , PHE I:156 , TYR I:225 , SER I:227 , HOH I:586
BINDING SITE FOR RESIDUE IPA I 406
24
FC3
SOFTWARE
SER F:217 , HOH F:745 , HOH F:757 , GLU J:49 , HOH J:740
BINDING SITE FOR RESIDUE CA J 401
25
FC4
SOFTWARE
GLY I:134 , GLY I:135 , TYR I:137 , TYR I:277 , VAL J:74 , ALA J:75 , SER J:76
BINDING SITE FOR RESIDUE EDO J 402
26
FC5
SOFTWARE
HIS J:154 , PHE J:156 , TYR J:225 , GLY J:226 , SER J:227 , HOH J:626
BINDING SITE FOR RESIDUE IPA J 403
27
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
28
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
29
GC1
SOFTWARE
LEU F:65 , TYR F:68 , ASP F:71 , GLN F:133 , GLY F:134 , HIS F:274 , ASN F:276 , TYR F:277 , HOH F:545 , HOH F:551 , HOH F:590 , HOH F:594 , HOH F:597 , HOH F:605 , HOH F:630 , HOH F:634 , HOH F:669 , HOH F:674 , HOH F:719 , HOH F:747 , SER G:76 , SER G:77 , LYS G:78
BINDING SITE FOR CHAIN F OF POLYSACCHARIDE RESIDUES 407 TO 409
30
GC2
SOFTWARE
LEU G:65 , TYR G:68 , ASP G:71 , GLN G:133 , GLY G:134 , HIS G:274 , ASN G:276 , TYR G:277 , ASN G:282 , HOH G:505 , HOH G:583 , HOH G:599 , HOH G:602 , HOH G:610 , HOH G:627 , HOH G:673 , HOH G:675 , HOH G:683 , HOH G:727 , HOH G:728 , SER H:76 , SER H:77 , LYS H:78
BINDING SITE FOR CHAIN G OF POLYSACCHARIDE RESIDUES 405 TO 407
31
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
32
GC4
SOFTWARE
LEU I:65 , TYR I:68 , ASP I:71 , GLN I:133 , GLY I:134 , HIS I:274 , ASN I:276 , TYR I:277 , ASN I:282 , HOH I:509 , HOH I:524 , HOH I:557 , HOH I:573 , HOH I:611 , HOH I:630 , HOH I:631 , HOH I:635 , HOH I:647 , HOH I:665 , HOH I:759 , SER J:76 , SER J:77 , LYS J:78
BINDING SITE FOR CHAIN I OF POLYSACCHARIDE RESIDUES 407 TO 409
33
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
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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_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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Organisms
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(
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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
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all CATH domains
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Pfam Domains
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