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4FMJ
Biol. Unit 6
Info
Asym.Unit (1.8 MB)
Biol.Unit 1 (455 KB)
Biol.Unit 2 (455 KB)
Biol.Unit 3 (456 KB)
Biol.Unit 4 (454 KB)
Biol.Unit 5 (901 KB)
Biol.Unit 6 (897 KB)
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(1)
Title
:
MERKEL CELL POLYOMAVIRUS VP1 IN COMPLEX WITH GD1A OLIGOSACCHARIDE
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
:
2.40
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
[
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Hetero Components
(3, 9)
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)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
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
3
Ligand/Ion
BETA-D-GALACTOSE
3
GOL
3
Ligand/Ion
GLYCEROL
4
SIA
3
Ligand/Ion
O-SIALIC ACID
[
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]
Sites
(20, 20)
Info
All Sites
01: AC8 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: DC1 (SOFTWARE)
08: DC2 (SOFTWARE)
09: DC3 (SOFTWARE)
10: DC4 (SOFTWARE)
11: DC5 (SOFTWARE)
12: DC6 (SOFTWARE)
13: DC7 (SOFTWARE)
14: DC8 (SOFTWARE)
15: DC9 (SOFTWARE)
16: EC1 (SOFTWARE)
17: EC2 (SOFTWARE)
18: EC3 (SOFTWARE)
19: EC4 (SOFTWARE)
20: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC8
SOFTWARE
HIS F:164 , SER F:246 , ILE F:247 , HOH F:772
BINDING SITE FOR RESIDUE CL F 601
02
AC9
SOFTWARE
HIS G:164 , SER G:246 , ILE G:247 , HOH G:770 , HOH G:773
BINDING SITE FOR RESIDUE CL G 601
03
BC1
SOFTWARE
TRP H:76 , ASP H:82 , LYS H:295 , SER H:297 , LYS H:299
BINDING SITE FOR RESIDUE SIA H 401
04
BC2
SOFTWARE
ASN H:162 , HIS H:164 , SER H:246 , ILE H:247
BINDING SITE FOR RESIDUE CL H 402
05
BC3
SOFTWARE
HIS I:164 , SER I:246 , ILE I:247 , GLN I:248 , HOH I:740 , HOH I:743
BINDING SITE FOR RESIDUE CL I 601
06
BC4
SOFTWARE
HIS J:164 , SER J:246 , ILE J:247 , HOH J:749 , HOH J:751
BINDING SITE FOR RESIDUE CL J 601
07
DC1
SOFTWARE
ASN P:162 , GLN P:248 , PRO P:254 , THR P:255 , VAL P:256 , CL P:402 , HOH P:560
BINDING SITE FOR RESIDUE GOL P 401
08
DC2
SOFTWARE
HIS P:164 , SER P:246 , GOL P:401 , HOH P:578
BINDING SITE FOR RESIDUE CL P 402
09
DC3
SOFTWARE
TRP Q:76 , ASP Q:82 , LYS Q:295 , SER Q:297 , LYS Q:299 , GAL Q:402 , HOH Q:534
BINDING SITE FOR RESIDUE SIA Q 401
10
DC4
SOFTWARE
SIA Q:401
BINDING SITE FOR RESIDUE GAL Q 402
11
DC5
SOFTWARE
HIS Q:164 , GLN Q:248 , PRO Q:254 , THR Q:255 , VAL Q:256 , CL Q:404
BINDING SITE FOR RESIDUE GOL Q 403
12
DC6
SOFTWARE
HIS Q:164 , SER Q:246 , GOL Q:403
BINDING SITE FOR RESIDUE CL Q 404
13
DC7
SOFTWARE
HIS R:164 , SER R:246 , ILE R:247 , HOH R:764 , HOH R:765
BINDING SITE FOR RESIDUE CL R 601
14
DC8
SOFTWARE
TRP S:76 , TYR S:81 , ASP S:82 , LYS S:295 , SER S:297 , LYS S:299 , GAL S:402 , HOH S:520
BINDING SITE FOR RESIDUE SIA S 401
15
DC9
SOFTWARE
SIA S:401
BINDING SITE FOR RESIDUE GAL S 402
16
EC1
SOFTWARE
HIS S:164 , SER S:246 , HOH S:558 , HOH S:560
BINDING SITE FOR RESIDUE CL S 403
17
EC2
SOFTWARE
TRP T:76 , TYR T:81 , ASP T:82 , LYS T:295 , SER T:297 , LYS T:299 , GAL T:402 , HOH T:537 , HOH T:548
BINDING SITE FOR RESIDUE SIA T 401
18
EC3
SOFTWARE
SIA T:401
BINDING SITE FOR RESIDUE GAL T 402
19
EC4
SOFTWARE
ASN T:162 , HIS T:164 , GLN T:248 , PRO T:254 , THR T:255 , VAL T:256 , CL T:404
BINDING SITE FOR RESIDUE GOL T 403
20
EC5
SOFTWARE
HIS T:164 , SER T:246 , ILE T:247 , GOL T:403 , HOH T:549
BINDING SITE FOR RESIDUE CL T 404
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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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_d4fmja_ (A:)
1b: SCOP_d4fmjb_ (B:)
1c: SCOP_d4fmjc_ (C:)
1d: SCOP_d4fmjd_ (D:)
1e: SCOP_d4fmje_ (E:)
1f: SCOP_d4fmjf_ (F:)
1g: SCOP_d4fmjg_ (G:)
1h: SCOP_d4fmjh_ (H:)
1i: SCOP_d4fmji_ (I:)
1j: SCOP_d4fmjj_ (J:)
1k: SCOP_d4fmjk_ (K:)
1l: SCOP_d4fmjl_ (L:)
1m: SCOP_d4fmjm_ (M:)
1n: SCOP_d4fmjn_ (N:)
1o: SCOP_d4fmjo_ (O:)
1p: SCOP_d4fmjp_ (P:)
1q: SCOP_d4fmjq_ (Q:)
1r: SCOP_d4fmjr_ (R:)
1s: SCOP_d4fmjs_ (S:)
1t: SCOP_d4fmjt_ (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
d4fmja_
A:
1b
d4fmjb_
B:
1c
d4fmjc_
C:
1d
d4fmjd_
D:
1e
d4fmje_
E:
1f
d4fmjf_
F:
1g
d4fmjg_
G:
1h
d4fmjh_
H:
1i
d4fmji_
I:
1j
d4fmjj_
J:
1k
d4fmjk_
K:
1l
d4fmjl_
L:
1m
d4fmjm_
M:
1n
d4fmjn_
N:
1o
d4fmjo_
O:
1p
d4fmjp_
P:
1q
d4fmjq_
Q:
1r
d4fmjr_
R:
1s
d4fmjs_
S:
1t
d4fmjt_
T:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
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Sorry, no Info available
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Chain R
Chain S
Chain T
Asymmetric Unit 1
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Asym.Unit (1.8 MB)
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