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4POT
Biol. Unit 1
Info
Asym.Unit (912 KB)
Biol.Unit 1 (450 KB)
Biol.Unit 2 (452 KB)
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(1)
Title
:
STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WITH N-GLYCOLYLNEURAMINIC ACID CONTAINING 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
:
2.10
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
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Hetero Components
(5, 34)
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)
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)
3j: BETA-D-GALACTOSE (GALj)
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)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
6a: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCa)
6b: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCb)
6c: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCc)
6d: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCd)
6e: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCe)
6f: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCf)
6g: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCg)
6h: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCh)
6i: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCi)
6j: 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMIN... (NGCj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
EDO
14
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
NGC
5
Ligand/Ion
3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC ACID
[
close Hetero Component info
]
Sites
(32, 32)
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: DC4 (SOFTWARE)
26: DC6 (SOFTWARE)
27: FC5 (SOFTWARE)
28: FC6 (SOFTWARE)
29: FC7 (SOFTWARE)
30: FC8 (SOFTWARE)
31: FC9 (SOFTWARE)
32: GC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:49 , SER B:217 , HOH B:621
BINDING SITE FOR RESIDUE CA A 401
02
AC2
SOFTWARE
GLY A:134 , GLY A:135 , TYR A:137 , TYR A:277 , HOH A:575 , VAL B:74 , ALA B:75 , SER B:76
BINDING SITE FOR RESIDUE EDO A 402
03
AC3
SOFTWARE
VAL A:122 , MET A:238 , GLN A:239 , HOH A:699
BINDING SITE FOR RESIDUE EDO A 403
04
AC4
SOFTWARE
HIS A:154 , PHE A:156 , TYR A:225 , GLY A:226 , SER A:227 , HOH A:699
BINDING SITE FOR RESIDUE IPA A 404
05
AC5
SOFTWARE
GLU B:49 , HOH B:640 , HOH B:698 , SER C:217 , HOH C:549 , HOH C:574
BINDING SITE FOR RESIDUE CA B 401
06
AC6
SOFTWARE
VAL B:122 , HIS B:154 , MET B:238 , GLN B:239 , HOH B:555
BINDING SITE FOR RESIDUE EDO B 402
07
AC7
SOFTWARE
LYS B:119 , ASN B:242 , HOH B:687 , ASN C:219 , GLU C:220 , ARG C:223
BINDING SITE FOR RESIDUE EDO B 403
08
AC8
SOFTWARE
HIS B:154 , PHE B:156 , TYR B:225 , GLY B:226 , SER B:227 , HOH B:555
BINDING SITE FOR RESIDUE IPA B 404
09
AC9
SOFTWARE
GLU C:49 , HOH C:623 , SER D:217 , HOH D:599 , HOH D:682
BINDING SITE FOR RESIDUE CA C 401
10
BC1
SOFTWARE
ARG C:39 , THR C:109 , THR G:109 , EDO G:402
BINDING SITE FOR RESIDUE EDO C 402
11
BC2
SOFTWARE
TYR B:51 , MET B:123 , LYS C:198 , ASP C:215 , SER C:217
BINDING SITE FOR RESIDUE EDO C 403
12
BC3
SOFTWARE
HIS C:154 , MET C:238 , GLN C:239 , HOH C:503 , HOH C:582
BINDING SITE FOR RESIDUE EDO C 404
13
BC4
SOFTWARE
GLY C:134 , GLY C:135 , TYR C:137 , TYR C:277 , HOH C:589 , HOH C:640 , ALA D:75 , SER D:76
BINDING SITE FOR RESIDUE EDO C 405
14
BC5
SOFTWARE
PHE C:156 , TYR C:225 , GLY C:226 , SER C:227
BINDING SITE FOR RESIDUE IPA C 406
15
BC6
SOFTWARE
GLU D:49 , SER E:217 , HOH E:582
BINDING SITE FOR RESIDUE CA D 401
16
BC7
SOFTWARE
GLU D:220 , ASN D:221 , ARG D:223 , ASP D:250 , GLY D:255 , HOH D:683
BINDING SITE FOR RESIDUE EDO D 402
17
BC8
SOFTWARE
ARG D:39 , THR D:109 , VAL D:298 , ARG F:39 , ASP F:108 , THR F:109
BINDING SITE FOR RESIDUE EDO D 403
18
BC9
SOFTWARE
HIS D:154 , MET D:238 , GLN D:239 , HOH D:518
BINDING SITE FOR RESIDUE EDO D 404
19
CC1
SOFTWARE
GLY D:140 , SER D:141 , SER D:142 , SER E:278 , GLU E:279
BINDING SITE FOR RESIDUE EDO D 405
20
CC2
SOFTWARE
HIS D:154 , PHE D:156 , GLY D:226 , SER D:227 , HOH D:518
BINDING SITE FOR RESIDUE IPA D 406
21
CC3
SOFTWARE
SER A:217 , HOH A:524 , HOH A:658 , GLU E:49 , HOH E:501
BINDING SITE FOR RESIDUE CA E 401
22
CC4
SOFTWARE
TYR D:51 , GLN E:166 , LYS E:198 , SER E:217
BINDING SITE FOR RESIDUE EDO E 402
23
CC5
SOFTWARE
HIS E:154 , MET E:238 , GLN E:239 , HOH E:659
BINDING SITE FOR RESIDUE EDO E 403
24
CC6
SOFTWARE
HIS E:154 , PHE E:156 , GLY E:226 , SER E:227 , HOH E:613 , HOH E:659
BINDING SITE FOR RESIDUE IPA E 404
25
DC4
SOFTWARE
THR C:109 , EDO C:402 , ARG G:39 , THR G:109
BINDING SITE FOR RESIDUE EDO G 402
26
DC6
SOFTWARE
THR B:62 , GLU B:64 , TYR G:137 , TYR G:277 , HOH G:668 , HOH G:680
BINDING SITE FOR RESIDUE EDO G 404
27
FC5
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:515 , HOH A:518 , HOH A:565 , HOH A:575 , HOH A:592 , HOH A:632 , HOH A:648 , SER B:77 , LYS B:78
BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 405 TO 407
28
FC6
SOFTWARE
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:527 , HOH B:528 , HOH B:535 , HOH B:591 , HOH B:595 , HOH B:601 , HOH B:617 , HOH B:647 , HOH B:666 , HOH B:671 , HOH B:721 , SER C:76 , SER C:77 , LYS C:78
BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 405 TO 407
29
FC7
SOFTWARE
LEU C:65 , TYR C:68 , ASP C:71 , GLN C:133 , GLY C:134 , HIS C:274 , ASN C:276 , TYR C:277 , ASN C:282 , HOH C:525 , HOH C:548 , HOH C:583 , HOH C:589 , HOH C:590 , HOH C:641 , HOH C:658 , HOH C:664 , HOH C:667 , HOH C:701 , HOH C:720 , HOH C:724 , HOH C:729 , SER D:76 , SER D:77 , LYS D:78 , HOH D:591 , ARG G:55 , ASN G:59 , ASN G:60 , PRO G:61 , ASP G:204
BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 407 TO 409
30
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:524 , HOH D:553 , HOH D:565 , HOH D:597 , HOH D:609 , HOH D:611 , HOH D:654 , HOH D:709 , HOH D:710 , HOH D:723 , SER E:76 , SER E:77 , LYS E:78 , HOH E:612 , MET G:105
BINDING SITE FOR CHAIN D OF POLYSACCHARIDE RESIDUES 407 TO 409
31
FC9
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:539 , HOH E:540 , HOH E:560 , HOH E:567 , HOH E:579 , HOH E:619 , HOH E:635 , HOH E:651 , HOH E:692 , GLU H:49 , HOH I:728
BINDING SITE FOR CHAIN E OF POLYSACCHARIDE RESIDUES 405 TO 407
32
GC5
SOFTWARE
GLU B:103 , SER F:76 , SER F:77 , LYS F:78 , HOH F:529 , 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:521 , HOH J:549 , HOH J:550 , HOH J:560 , HOH J:564 , HOH J:574 , HOH J:635 , HOH J:636 , HOH J:664 , HOH J:719
BINDING SITE FOR CHAIN J OF POLYSACCHARIDE RESIDUES 406 TO 408
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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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_d4pota_ (A:)
1b: SCOP_d4potb_ (B:)
1c: SCOP_d4potc_ (C:)
1d: SCOP_d4potd_ (D:)
1e: SCOP_d4pote_ (E:)
1f: SCOP_d4potf_ (F:)
1g: SCOP_d4potg_ (G:)
1h: SCOP_d4poth_ (H:)
1i: SCOP_d4poti_ (I:)
1j: SCOP_d4potj_ (J:)
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Protein Domains
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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
d4pota_
A:
1b
d4potb_
B:
1c
d4potc_
C:
1d
d4potd_
D:
1e
d4pote_
E:
1f
d4potf_
F:
1g
d4potg_
G:
1h
d4poth_
H:
1i
d4poti_
I:
1j
d4potj_
J:
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CATH Domains
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Pfam Domains
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Asym.Unit (912 KB)
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