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4FMI
Asym. Unit
Info
Asym.Unit (1.8 MB)
Biol.Unit 1 (463 KB)
Biol.Unit 2 (466 KB)
Biol.Unit 3 (468 KB)
Biol.Unit 4 (466 KB)
Biol.Unit 5 (918 KB)
Biol.Unit 6 (919 KB)
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(1)
Title
:
MERKEL CELL POLYOMAVIRUS VP1 IN COMPLEX WITH 3'-SIALYLLACTOSAMINE
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
:
2.00
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
]
Hetero Components
(5, 53)
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)
1u: CHLORIDE ION (CLu)
2a: BETA-D-GALACTOSE (GALa)
2b: BETA-D-GALACTOSE (GALb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
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)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5a: O-SIALIC ACID (SIAa)
5b: O-SIALIC ACID (SIAb)
5c: O-SIALIC ACID (SIAc)
5d: O-SIALIC ACID (SIAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
21
Ligand/Ion
CHLORIDE ION
2
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
3
GOL
25
Ligand/Ion
GLYCEROL
4
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SIA
4
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(53, 53)
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: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:76 , ASP A:82 , LYS A:295 , SER A:297 , LYS A:299 , GAL A:403 , HOH A:659 , HOH A:660 , LYS Q:86 , HOH Q:673
BINDING SITE FOR RESIDUE SIA A 401
02
AC2
SOFTWARE
GAL A:403 , GLN Q:92 , PRO Q:93 , PRO Q:187 , LYS Q:188 , HOH Q:553 , HOH Q:623 , HOH Q:678
BINDING SITE FOR RESIDUE NAG A 402
03
AC3
SOFTWARE
SER A:297 , SIA A:401 , NAG A:402 , HOH A:671 , HOH A:679 , GLN Q:92
BINDING SITE FOR RESIDUE GAL A 403
04
AC4
SOFTWARE
ASN A:162 , GLN A:248 , PRO A:254 , THR A:255 , VAL A:256 , CL A:405 , HOH A:531 , HOH A:629
BINDING SITE FOR RESIDUE GOL A 404
05
AC5
SOFTWARE
HIS A:164 , SER A:246 , ILE A:247 , GOL A:404
BINDING SITE FOR RESIDUE CL A 405
06
AC6
SOFTWARE
ASN B:162 , HIS B:164 , GLN B:248 , PRO B:254 , THR B:255 , VAL B:256 , CL B:402 , HOH B:654
BINDING SITE FOR RESIDUE GOL B 401
07
AC7
SOFTWARE
HIS B:164 , SER B:246 , ILE B:247 , GLN B:248 , GOL B:401 , HOH B:504
BINDING SITE FOR RESIDUE CL B 402
08
AC8
SOFTWARE
ASN C:162 , HIS C:164 , GLN C:248 , PRO C:254 , THR C:255 , VAL C:256 , CL C:402 , HOH C:556
BINDING SITE FOR RESIDUE GOL C 401
09
AC9
SOFTWARE
HIS C:164 , SER C:246 , ILE C:247 , GLN C:248 , GOL C:401 , HOH C:547
BINDING SITE FOR RESIDUE CL C 402
10
BC1
SOFTWARE
ASN D:162 , HIS D:164 , GLN D:248 , PRO D:254 , THR D:255 , VAL D:256 , CL D:402 , HOH D:591 , HOH D:601
BINDING SITE FOR RESIDUE GOL D 401
11
BC2
SOFTWARE
HIS D:164 , SER D:246 , ILE D:247 , GLN D:248 , GOL D:401 , HOH D:508
BINDING SITE FOR RESIDUE CL D 402
12
BC3
SOFTWARE
TRP E:76 , TYR E:81 , ASP E:82 , LYS E:295 , SER E:297 , LYS E:299 , HOH E:620 , HOH E:660 , HOH E:661
BINDING SITE FOR RESIDUE SIA E 401
13
BC4
SOFTWARE
ASN E:162 , GLN E:248 , PRO E:254 , VAL E:256 , CL E:403 , HOH E:591 , HOH E:666
BINDING SITE FOR RESIDUE GOL E 402
14
BC5
SOFTWARE
HIS E:164 , SER E:246 , ILE E:247 , GOL E:402 , HOH E:603
BINDING SITE FOR RESIDUE CL E 403
15
BC6
SOFTWARE
ASN F:162 , HIS F:164 , SER F:246 , GLN F:248 , PRO F:254 , THR F:255 , VAL F:256 , CL F:402
BINDING SITE FOR RESIDUE GOL F 401
16
BC7
SOFTWARE
ASN F:162 , HIS F:164 , SER F:246 , ILE F:247 , GOL F:401 , HOH F:517
BINDING SITE FOR RESIDUE CL F 402
17
BC8
SOFTWARE
ASN G:162 , GLN G:248 , PRO G:254 , THR G:255 , VAL G:256 , CL G:402
BINDING SITE FOR RESIDUE GOL G 401
18
BC9
SOFTWARE
HIS G:164 , SER G:246 , ILE G:247 , GLN G:248 , GOL G:401 , HOH G:519
BINDING SITE FOR RESIDUE CL G 402
19
CC1
SOFTWARE
ASN H:162 , GLN H:248 , PRO H:254 , THR H:255 , VAL H:256 , CL H:402
BINDING SITE FOR RESIDUE GOL H 401
20
CC2
SOFTWARE
HIS H:164 , SER H:246 , ILE H:247 , GLN H:248 , GOL H:401 , HOH H:503
BINDING SITE FOR RESIDUE CL H 402
21
CC3
SOFTWARE
ASN I:162 , HIS I:164 , GLN I:248 , PRO I:254 , THR I:255 , VAL I:256 , CL I:402
BINDING SITE FOR RESIDUE GOL I 401
22
CC4
SOFTWARE
HIS I:164 , SER I:246 , ILE I:247 , GLN I:248 , GOL I:401 , HOH I:536
BINDING SITE FOR RESIDUE CL I 402
23
CC5
SOFTWARE
ASN J:162 , HIS J:164 , GLN J:248 , PRO J:254 , THR J:255 , VAL J:256 , CL J:402
BINDING SITE FOR RESIDUE GOL J 401
24
CC6
SOFTWARE
HIS J:164 , SER J:246 , ILE J:247 , GOL J:401 , HOH J:533
BINDING SITE FOR RESIDUE CL J 402
25
CC7
SOFTWARE
ASN K:162 , HIS K:164 , GLN K:248 , PRO K:254 , VAL K:256 , CL K:402 , HOH K:565 , HOH K:636
BINDING SITE FOR RESIDUE GOL K 401
26
CC8
SOFTWARE
ASN K:162 , HIS K:164 , SER K:246 , ILE K:247 , GLN K:248 , GOL K:401 , HOH K:506
BINDING SITE FOR RESIDUE CL K 402
27
CC9
SOFTWARE
LYS K:217 , SER K:236 , THR M:116 , GLU O:56 , TYR O:58
BINDING SITE FOR RESIDUE GOL K 403
28
DC1
SOFTWARE
ASN L:75 , TRP L:76 , TYR L:143 , TRP L:144 , ASP M:181 , GLN M:183 , HOH M:575
BINDING SITE FOR RESIDUE GOL L 501
29
DC2
SOFTWARE
ASN L:162 , HIS L:164 , GLN L:248 , PRO L:254 , THR L:255 , VAL L:256 , CL L:504
BINDING SITE FOR RESIDUE GOL L 502
30
DC3
SOFTWARE
SER G:88 , TYR L:81 , ASP L:82 , LYS L:295 , HOH L:782
BINDING SITE FOR RESIDUE GOL L 503
31
DC4
SOFTWARE
HIS L:164 , SER L:246 , ILE L:247 , GLN L:248 , GOL L:502 , HOH L:612
BINDING SITE FOR RESIDUE CL L 504
32
DC5
SOFTWARE
TRP M:76 , TYR M:81 , ASP M:82 , LYS M:295 , SER M:297 , LYS M:299 , HOH M:551 , HOH M:558 , HOH M:612 , HOH M:630
BINDING SITE FOR RESIDUE SIA M 401
33
DC6
SOFTWARE
ASN M:75 , TRP M:76 , TYR M:143 , TRP M:144 , HOH M:720 , ASP N:181 , TYR N:182 , GLN N:183 , GLN N:210 , HOH N:532
BINDING SITE FOR RESIDUE GOL M 402
34
DC7
SOFTWARE
ASN M:162 , HIS M:164 , GLN M:248 , PRO M:254 , THR M:255 , VAL M:256 , CL M:404
BINDING SITE FOR RESIDUE GOL M 403
35
DC8
SOFTWARE
HIS M:164 , SER M:246 , ILE M:247 , GLN M:248 , GOL M:403 , HOH M:503
BINDING SITE FOR RESIDUE CL M 404
36
DC9
SOFTWARE
ASN N:162 , HIS N:164 , GLN N:248 , PRO N:254 , VAL N:256 , CL N:402 , HOH N:534
BINDING SITE FOR RESIDUE GOL N 401
37
EC1
SOFTWARE
HIS N:164 , SER N:246 , ILE N:247 , GOL N:401 , HOH N:525
BINDING SITE FOR RESIDUE CL N 402
38
EC2
SOFTWARE
ASN O:162 , GLN O:248 , PRO O:254 , THR O:255 , VAL O:256 , CL O:402 , HOH O:511
BINDING SITE FOR RESIDUE GOL O 401
39
EC3
SOFTWARE
SER O:246 , ILE O:247 , GLN O:248 , GOL O:401 , HOH O:504
BINDING SITE FOR RESIDUE CL O 402
40
EC4
SOFTWARE
ASN P:162 , HIS P:164 , GLN P:248 , PRO P:254 , THR P:255 , VAL P:256 , CL P:402 , HOH P:564
BINDING SITE FOR RESIDUE GOL P 401
41
EC5
SOFTWARE
ASN P:162 , HIS P:164 , SER P:246 , ILE P:247 , GOL P:401 , HOH P:534
BINDING SITE FOR RESIDUE CL P 402
42
EC6
SOFTWARE
ASN Q:162 , HIS Q:164 , GLN Q:248 , PRO Q:254 , THR Q:255 , VAL Q:256 , LEU Q:257 , CL Q:402 , HOH Q:590
BINDING SITE FOR RESIDUE GOL Q 401
43
EC7
SOFTWARE
HIS Q:164 , SER Q:246 , ILE Q:247 , GLN Q:248 , GOL Q:401 , HOH Q:515
BINDING SITE FOR RESIDUE CL Q 402
44
EC8
SOFTWARE
ASN R:75 , TRP R:76 , TYR R:143 , TRP R:144 , HOH R:802 , ASP S:181 , GLN S:183 , HOH S:568
BINDING SITE FOR RESIDUE GOL R 501
45
EC9
SOFTWARE
ASN R:162 , HIS R:164 , GLN R:248 , PRO R:254 , THR R:255 , VAL R:256 , CL R:503 , HOH R:801
BINDING SITE FOR RESIDUE GOL R 502
46
FC1
SOFTWARE
HIS R:164 , SER R:246 , ILE R:247 , GLN R:248 , GOL R:502 , HOH R:629
BINDING SITE FOR RESIDUE CL R 503
47
FC2
SOFTWARE
TYR D:81 , ASP D:82 , LYS S:86 , GLY S:87 , SER S:88
BINDING SITE FOR RESIDUE GOL S 401
48
FC3
SOFTWARE
HIS S:164 , SER S:246 , ILE S:247 , GLN S:248 , HOH S:517
BINDING SITE FOR RESIDUE CL S 402
49
FC4
SOFTWARE
ARG C:148 , TRP R:144 , HOH R:802 , SER S:89
BINDING SITE FOR RESIDUE CL S 403
50
FC5
SOFTWARE
TRP T:76 , TYR T:81 , ASP T:82 , LYS T:295 , SER T:297 , LYS T:299 , GAL T:402 , HOH T:603 , HOH T:612 , HOH T:674
BINDING SITE FOR RESIDUE SIA T 401
51
FC6
SOFTWARE
SIA T:401 , HOH T:635
BINDING SITE FOR RESIDUE GAL T 402
52
FC7
SOFTWARE
ASN T:162 , HIS T:164 , GLN T:248 , PRO T:254 , THR T:255 , VAL T:256 , CL T:404 , HOH T:623
BINDING SITE FOR RESIDUE GOL T 403
53
FC8
SOFTWARE
HIS T:164 , SER T:246 , ILE T:247 , GOL T:403 , HOH T:504
BINDING SITE FOR RESIDUE CL T 404
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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[
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 20)
Info
All SCOP Domains
1a: SCOP_d4fmia_ (A:)
1b: SCOP_d4fmib_ (B:)
1c: SCOP_d4fmik_ (K:)
1d: SCOP_d4fmil_ (L:)
1e: SCOP_d4fmim_ (M:)
1f: SCOP_d4fmin_ (N:)
1g: SCOP_d4fmio_ (O:)
1h: SCOP_d4fmip_ (P:)
1i: SCOP_d4fmiq_ (Q:)
1j: SCOP_d4fmir_ (R:)
1k: SCOP_d4fmis_ (S:)
1l: SCOP_d4fmit_ (T:)
1m: SCOP_d4fmic_ (C:)
1n: SCOP_d4fmid_ (D:)
1o: SCOP_d4fmie_ (E:)
1p: SCOP_d4fmif_ (F:)
1q: SCOP_d4fmig_ (G:)
1r: SCOP_d4fmih_ (H:)
1s: SCOP_d4fmii_ (I:)
1t: SCOP_d4fmij_ (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)
Merkel cell polyomavirus [TaxId: 493803]
(4)
1a
d4fmia_
A:
1b
d4fmib_
B:
1c
d4fmik_
K:
1d
d4fmil_
L:
1e
d4fmim_
M:
1f
d4fmin_
N:
1g
d4fmio_
O:
1h
d4fmip_
P:
1i
d4fmiq_
Q:
1j
d4fmir_
R:
1k
d4fmis_
S:
1l
d4fmit_
T:
1m
d4fmic_
C:
1n
d4fmid_
D:
1o
d4fmie_
E:
1p
d4fmif_
F:
1q
d4fmig_
G:
1r
d4fmih_
H:
1s
d4fmii_
I:
1t
d4fmij_
J:
[
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CATH Domains
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Asym.Unit (1.8 MB)
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Biol.Unit 1 (463 KB)
Header - Biol.Unit 1
Biol.Unit 2 (466 KB)
Header - Biol.Unit 2
Biol.Unit 3 (468 KB)
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Biol.Unit 4 (466 KB)
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