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Asym. Unit
Info
Asym.Unit (439 KB)
Biol.Unit 1 (428 KB)
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(1)
Title
:
JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GM1 OLIGOSACCHARIDE
Authors
:
L. J. Stroh, T. Stehle
Date
:
24 Nov 14 (Deposition) - 22 Apr 15 (Release) - 27 May 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Beta-Sandwich, Jelly-Roll, Viral Major Capsid Protein, Glycan, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. J. Stroh, M. S. Maginnis, B. S. Blaum, C. D. Nelson, U. Neu, G. V. Gee, B. A. O'Hara, N. Motamedi, D. Dimaio, W. J. Atwood, T. Stehle
The Greater Affinity Of Jc Polyomavirus Capsid For Alpha 2, 6-Linked Lactoseries Tetrasaccharide C Than For Other Sialylated Glycans Is A Major Determinant Of Infectivity.
J. Virol. V. 89 6364 2015
[
close entry info
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Hetero Components
(7, 39)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
2a: 1,2-ETHANEDIOL (EDOa)
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)
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)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
5a: POTASSIUM ION (Ka)
5b: POTASSIUM ION (Kb)
5c: POTASSIUM ION (Kc)
5d: POTASSIUM ION (Kd)
5e: POTASSIUM ION (Ke)
6a: N-ACETYL-D-GALACTOSAMINE (NGAa)
6b: N-ACETYL-D-GALACTOSAMINE (NGAb)
6c: N-ACETYL-D-GALACTOSAMINE (NGAc)
7a: O-SIALIC ACID (SIAa)
7b: O-SIALIC ACID (SIAb)
7c: O-SIALIC ACID (SIAc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
GAL
6
Ligand/Ion
BETA-D-GALACTOSE
4
GOL
5
Ligand/Ion
GLYCEROL
5
K
5
Ligand/Ion
POTASSIUM ION
6
NGA
3
Ligand/Ion
N-ACETYL-D-GALACTOSAMINE
7
SIA
3
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
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Sites
(28, 28)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:62 , SER A:69 , ASP A:70 , SER A:71 , MET A:76
binding site for residue GOL A 301
02
AC2
SOFTWARE
VAL A:225 , LEU A:226 , HIS A:227 , ARG A:276 , EDO A:304
binding site for residue EDO A 302
03
AC3
SOFTWARE
PHE A:144 , THR A:234 , HOH A:448
binding site for residue EDO A 303
04
AC4
SOFTWARE
HIS A:142 , GLY A:214 , THR A:215 , EDO A:302
binding site for residue EDO A 304
05
AC5
SOFTWARE
GLU A:208 , ASN A:209 , ARG A:211 , ASP A:238 , GLY A:243
binding site for residue EDO A 305
06
AC6
SOFTWARE
GLU A:40 , HOH A:516 , THR B:205 , GLU B:208 , HOH B:492
binding site for residue K A 306
07
AC7
SOFTWARE
THR A:205 , GLU A:208 , HOH A:493 , HOH A:507 , HOH A:510 , HOH A:515 , GLU E:40
binding site for residue K A 307
08
AC8
SOFTWARE
HIS A:121 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , MET B:76
binding site for residue GOL B 305
09
AC9
SOFTWARE
PHE B:144 , THR B:234 , EDO B:307 , HOH B:429
binding site for residue EDO B 306
10
AD1
SOFTWARE
THR B:215 , EDO B:306 , EDO B:308
binding site for residue EDO B 307
11
AD2
SOFTWARE
HIS B:227 , ARG B:276 , EDO B:307
binding site for residue EDO B 308
12
AD3
SOFTWARE
GLU B:40 , HOH B:524 , THR C:205 , GLU C:208 , HOH C:474
binding site for residue K B 309
13
AD4
SOFTWARE
HIS B:121 , SER C:62 , SER C:64 , SER C:69 , ASP C:70 , SER C:71 , PRO C:72 , MET C:76 , HOH C:401
binding site for residue GOL C 306
14
AD5
SOFTWARE
THR C:215 , EDO C:308 , HOH C:480
binding site for residue EDO C 307
15
AD6
SOFTWARE
EDO C:307
binding site for residue EDO C 308
16
AD7
SOFTWARE
GLU C:208 , ASN C:209 , ARG C:211 , ASP C:238 , VAL C:242 , GLY C:243
binding site for residue EDO C 309
17
AD8
SOFTWARE
GLU C:40 , THR D:205 , GLU D:208 , HOH D:522 , HOH D:619
binding site for residue K C 310
18
AD9
SOFTWARE
HIS C:121 , SER D:62 , SER D:64 , SER D:69 , ASP D:70 , SER D:71 , PRO D:72 , MET D:76 , HOH D:503
binding site for residue GOL D 306
19
AE1
SOFTWARE
HIS D:142 , THR D:215
binding site for residue EDO D 307
20
AE2
SOFTWARE
GLU D:208 , ASN D:209 , ARG D:211 , ASP D:238 , GLY D:243
binding site for residue EDO D 308
21
AE3
SOFTWARE
GLU D:40 , THR E:205 , GLU E:208 , HOH E:489 , HOH E:501
binding site for residue K D 309
22
AE4
SOFTWARE
ARG A:265 , THR B:66 , HIS D:121 , SER E:62 , SER E:64 , SER E:69 , ASP E:70 , SER E:71 , PRO E:72 , MET E:76 , HOH E:485
binding site for residue GOL E 301
23
AE5
SOFTWARE
THR E:234 , EDO E:304
binding site for residue EDO E 302
24
AE6
SOFTWARE
LEU E:43 , THR E:44 , GLU E:46 , ASN E:192
binding site for residue EDO E 303
25
AE7
SOFTWARE
GLY E:214 , THR E:215 , EDO E:302
binding site for residue EDO E 304
26
AE8
SOFTWARE
ASN A:130 , LEU B:54 , LYS B:59 , SER B:60 , ILE B:61 , SER B:62 , ASN B:123 , ASN B:264 , SER B:266 , SER B:268 , GLN B:270 , HOH B:403 , HOH B:423 , HOH B:425 , HOH B:468 , HOH B:491 , PHE C:67 , HOH C:490 , GLU E:52
binding site for Poly-Saccharide residues SIA B 301 through GAL B 304
27
AE9
SOFTWARE
HIS A:121 , ASN A:130 , LEU B:54 , LYS B:59 , SER B:60 , ILE B:61 , SER B:62 , SER B:64 , SER B:69 , ASP B:70 , SER B:71 , PRO B:72 , MET B:76 , ASN B:123 , ASN B:130 , ASN B:264 , SER B:266 , SER B:268 , GLN B:270 , HOH B:403 , HOH B:423 , HOH B:425 , HOH B:468 , HOH B:491 , LEU C:54 , LYS C:59 , SER C:60 , ILE C:61 , SER C:62 , PHE C:67 , ASN C:123 , ASN C:264 , SER C:266 , SER C:268 , GLN C:270 , HOH C:419 , HOH C:422 , HOH C:425 , HOH C:428 , HOH C:468 , HOH C:490 , HOH C:500 , PHE D:67 , GLU E:52
binding site for Poly-Saccharide residues SIA C 301 through BGC C 305
28
AF1
SOFTWARE
ASN B:130 , LEU C:54 , LYS C:59 , SER C:60 , ILE C:61 , SER C:62 , ASN C:123 , ASN C:130 , ASN C:264 , SER C:266 , SER C:268 , GLN C:270 , HOH C:419 , HOH C:422 , HOH C:425 , HOH C:428 , HOH C:468 , HOH C:500 , LEU D:54 , LYS D:59 , SER D:60 , SER D:62 , PHE D:67 , ASN D:123 , ASN D:264 , SER D:266 , SER D:268 , GLN D:270 , HOH D:509 , HOH D:531 , HOH D:567 , PHE E:67
binding site for Poly-Saccharide residues SIA D 301 through BGC D 305
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Exons
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SCOP Domains
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CATH Domains
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Pfam Domains
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