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4FMH
Biol. Unit 2
Info
Asym.Unit (1.8 MB)
Biol.Unit 1 (478 KB)
Biol.Unit 2 (477 KB)
Biol.Unit 3 (481 KB)
Biol.Unit 4 (475 KB)
Biol.Unit 5 (946 KB)
Biol.Unit 6 (938 KB)
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(1)
Title
:
MERKEL CELL POLYOMAVIRUS VP1 IN COMPLEX WITH DISIALYLLACTOSE
Authors
:
U. Neu, H. Hengel, T. Stehle
Date
:
17 Jun 12 (Deposition) - 05 Sep 12 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Biol. Unit 3: K,L,M,N,O (1x)
Biol. Unit 4: P,Q,R,S,T (1x)
Biol. Unit 5: A,B,C,D,E,K,L,M,N,O (1x)
Biol. Unit 6: F,G,H,I,J,P,Q,R,S,T (1x)
Keywords
:
Viral Capsid Protein, Jelly Roll, Encapsidation, Receptor Binding, Sialylated Oligosaccharides, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Neu, H. Hengel, B. S. Blaum, R. M. Schowalter, D. Macejak, M. Gilbert W. W. Wakarchuk, A. Imamura, H. Ando, M. Kiso, N. Arnberg, R. L. Garcea, T. Peters, C. B. Buck, T. Stehle
Structures Of Merkel Cell Polyomavirus Vp1 Complexes Define A Sialic Acid Binding Site Required For Infection.
Plos Pathog. V. 8 02738 2012
[
close entry info
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
1h: CHLORIDE ION (CLh)
1i: CHLORIDE ION (CLi)
1j: CHLORIDE ION (CLj)
1k: CHLORIDE ION (CLk)
1l: CHLORIDE ION (CLl)
1m: CHLORIDE ION (CLm)
1n: CHLORIDE ION (CLn)
1o: CHLORIDE ION (CLo)
1p: CHLORIDE ION (CLp)
1q: CHLORIDE ION (CLq)
1r: CHLORIDE ION (CLr)
1s: CHLORIDE ION (CLs)
1t: CHLORIDE ION (CLt)
2a: BETA-D-GALACTOSE (GALa)
2b: BETA-D-GALACTOSE (GALb)
2c: BETA-D-GALACTOSE (GALc)
2d: BETA-D-GALACTOSE (GALd)
2e: BETA-D-GALACTOSE (GALe)
2f: BETA-D-GALACTOSE (GALf)
2g: BETA-D-GALACTOSE (GALg)
3a: GLYCEROL (GOLa)
3aa: GLYCEROL (GOLaa)
3ab: GLYCEROL (GOLab)
3ac: GLYCEROL (GOLac)
3ad: GLYCEROL (GOLad)
3ae: GLYCEROL (GOLae)
3af: GLYCEROL (GOLaf)
3ag: GLYCEROL (GOLag)
3ah: GLYCEROL (GOLah)
3ai: GLYCEROL (GOLai)
3aj: GLYCEROL (GOLaj)
3ak: GLYCEROL (GOLak)
3al: GLYCEROL (GOLal)
3am: GLYCEROL (GOLam)
3an: GLYCEROL (GOLan)
3ao: GLYCEROL (GOLao)
3ap: GLYCEROL (GOLap)
3aq: GLYCEROL (GOLaq)
3ar: GLYCEROL (GOLar)
3as: GLYCEROL (GOLas)
3at: GLYCEROL (GOLat)
3au: GLYCEROL (GOLau)
3av: GLYCEROL (GOLav)
3aw: GLYCEROL (GOLaw)
3ax: GLYCEROL (GOLax)
3ay: GLYCEROL (GOLay)
3az: GLYCEROL (GOLaz)
3b: GLYCEROL (GOLb)
3ba: GLYCEROL (GOLba)
3bb: GLYCEROL (GOLbb)
3bc: GLYCEROL (GOLbc)
3bd: GLYCEROL (GOLbd)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
3w: GLYCEROL (GOLw)
3x: GLYCEROL (GOLx)
3y: GLYCEROL (GOLy)
3z: GLYCEROL (GOLz)
4a: O-SIALIC ACID (SIAa)
4b: O-SIALIC ACID (SIAb)
4c: O-SIALIC ACID (SIAc)
4d: O-SIALIC ACID (SIAd)
4e: O-SIALIC ACID (SIAe)
4f: O-SIALIC ACID (SIAf)
4g: O-SIALIC ACID (SIAg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GAL
1
Ligand/Ion
BETA-D-GALACTOSE
3
GOL
10
Ligand/Ion
GLYCEROL
4
SIA
1
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: CC3 (SOFTWARE)
02: CC4 (SOFTWARE)
03: CC5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: DC3 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC5 (SOFTWARE)
13: DC6 (SOFTWARE)
14: DC7 (SOFTWARE)
15: DC8 (SOFTWARE)
16: DC9 (SOFTWARE)
17: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC3
SOFTWARE
ASN F:162 , GLN F:248 , PRO F:254 , THR F:255 , VAL F:256 , CL F:403 , HOH F:611
BINDING SITE FOR RESIDUE GOL F 401
02
CC4
SOFTWARE
LYS F:147 , ARG F:148 , ASP F:151 , HOH F:513 , HOH F:530
BINDING SITE FOR RESIDUE GOL F 402
03
CC5
SOFTWARE
ASN F:162 , HIS F:164 , SER F:246 , ILE F:247 , GLN F:248 , GOL F:401 , HOH F:520
BINDING SITE FOR RESIDUE CL F 403
04
CC6
SOFTWARE
ASN G:162 , HIS G:164 , GLN G:248 , PRO G:254 , THR G:255 , VAL G:256 , CL G:403 , HOH G:696
BINDING SITE FOR RESIDUE GOL G 401
05
CC7
SOFTWARE
LYS G:147 , ARG G:148 , ASP G:151 , HOH G:673 , HOH G:714
BINDING SITE FOR RESIDUE GOL G 402
06
CC8
SOFTWARE
HIS G:164 , SER G:246 , ILE G:247 , GLN G:248 , GOL G:401 , HOH G:518
BINDING SITE FOR RESIDUE CL G 403
07
CC9
SOFTWARE
TRP H:76 , ASP H:82 , LYS H:295 , SER H:297 , LYS H:299 , GAL H:402 , HOH H:593 , HOH H:627 , HOH H:635
BINDING SITE FOR RESIDUE SIA H 401
08
DC1
SOFTWARE
SIA H:401 , HOH H:632 , HOH H:688
BINDING SITE FOR RESIDUE GAL H 402
09
DC2
SOFTWARE
ASN H:162 , GLN H:248 , PRO H:254 , THR H:255 , VAL H:256 , CL H:405 , HOH H:685
BINDING SITE FOR RESIDUE GOL H 403
10
DC3
SOFTWARE
LYS H:147 , ARG H:148 , ASP H:151 , HOH H:641 , HOH H:669
BINDING SITE FOR RESIDUE GOL H 404
11
DC4
SOFTWARE
HIS H:164 , SER H:246 , ILE H:247 , GOL H:403 , HOH H:503
BINDING SITE FOR RESIDUE CL H 405
12
DC5
SOFTWARE
ASN I:162 , HIS I:164 , GLN I:248 , PRO I:254 , THR I:255 , VAL I:256 , CL I:403
BINDING SITE FOR RESIDUE GOL I 401
13
DC6
SOFTWARE
LYS I:147 , ARG I:148 , HIS I:150 , ASP I:151 , HOH I:545 , HOH I:599 , HOH I:665
BINDING SITE FOR RESIDUE GOL I 402
14
DC7
SOFTWARE
HIS I:164 , SER I:246 , ILE I:247 , GLN I:248 , GOL I:401 , HOH I:533
BINDING SITE FOR RESIDUE CL I 403
15
DC8
SOFTWARE
ASN J:162 , HIS J:164 , GLN J:248 , PRO J:254 , THR J:255 , VAL J:256 , CL J:403 , HOH J:672 , HOH J:683
BINDING SITE FOR RESIDUE GOL J 401
16
DC9
SOFTWARE
LYS J:147 , ARG J:148 , HIS J:150 , ASP J:151 , HOH J:639
BINDING SITE FOR RESIDUE GOL J 402
17
EC1
SOFTWARE
HIS J:164 , SER J:246 , ILE J:247 , GOL J:401 , HOH J:534
BINDING SITE FOR RESIDUE CL J 403
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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, 20)
Info
All SCOP Domains
1a: SCOP_d4fmha_ (A:)
1b: SCOP_d4fmhb_ (B:)
1c: SCOP_d4fmhc_ (C:)
1d: SCOP_d4fmhd_ (D:)
1e: SCOP_d4fmhe_ (E:)
1f: SCOP_d4fmhf_ (F:)
1g: SCOP_d4fmhg_ (G:)
1h: SCOP_d4fmhh_ (H:)
1i: SCOP_d4fmhi_ (I:)
1j: SCOP_d4fmhj_ (J:)
1k: SCOP_d4fmhk_ (K:)
1l: SCOP_d4fmhl_ (L:)
1m: SCOP_d4fmhm_ (M:)
1n: SCOP_d4fmhn_ (N:)
1o: SCOP_d4fmho_ (O:)
1p: SCOP_d4fmhp_ (P:)
1q: SCOP_d4fmhq_ (Q:)
1r: SCOP_d4fmhr_ (R:)
1s: SCOP_d4fmhs_ (S:)
1t: SCOP_d4fmht_ (T:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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)
Merkel cell polyomavirus [TaxId: 493803]
(4)
1a
d4fmha_
A:
1b
d4fmhb_
B:
1c
d4fmhc_
C:
1d
d4fmhd_
D:
1e
d4fmhe_
E:
1f
d4fmhf_
F:
1g
d4fmhg_
G:
1h
d4fmhh_
H:
1i
d4fmhi_
I:
1j
d4fmhj_
J:
1k
d4fmhk_
K:
1l
d4fmhl_
L:
1m
d4fmhm_
M:
1n
d4fmhn_
N:
1o
d4fmho_
O:
1p
d4fmhp_
P:
1q
d4fmhq_
Q:
1r
d4fmhr_
R:
1s
d4fmhs_
S:
1t
d4fmht_
T:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
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Protein
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Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (1.8 MB)
Header - Asym.Unit
Biol.Unit 1 (478 KB)
Header - Biol.Unit 1
Biol.Unit 2 (477 KB)
Header - Biol.Unit 2
Biol.Unit 3 (481 KB)
Header - Biol.Unit 3
Biol.Unit 4 (475 KB)
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Biol.Unit 5 (946 KB)
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