PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
4FMH
Biol. Unit 1
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)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
]
Hetero Components
(3, 15)
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
13
Ligand/Ion
GLYCEROL
4
SIA
1
Ligand/Ion
O-SIALIC ACID
[
close Hetero Component info
]
Sites
(21, 21)
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: JC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:75 , TRP A:76 , TYR A:143 , TRP A:144 , HOH A:782 , ASP B:181 , GLN B:183 , HOH B:562 , HOH B:691
BINDING SITE FOR RESIDUE GOL A 501
02
AC2
SOFTWARE
ASN A:162 , HIS A:164 , GLN A:248 , PRO A:254 , THR A:255 , VAL A:256 , CL A:504 , HOH A:635 , HOH A:790 , HOH A:791
BINDING SITE FOR RESIDUE GOL A 502
03
AC3
SOFTWARE
LYS A:147 , ARG A:148 , HIS A:150 , ASP A:151 , HOH A:662
BINDING SITE FOR RESIDUE GOL A 503
04
AC4
SOFTWARE
HIS A:164 , SER A:246 , ILE A:247 , GLN A:248 , GOL A:502 , HOH A:606
BINDING SITE FOR RESIDUE CL A 504
05
AC5
SOFTWARE
TRP B:76 , TYR B:81 , ASP B:82 , LYS B:295 , SER B:297 , LYS B:299 , GAL B:402 , HOH B:608 , HOH B:624 , HOH B:704
BINDING SITE FOR RESIDUE SIA B 401
06
AC6
SOFTWARE
SIA B:401 , HOH B:572 , HOH B:692
BINDING SITE FOR RESIDUE GAL B 402
07
AC7
SOFTWARE
ASN B:162 , GLN B:248 , PRO B:254 , THR B:255 , VAL B:256 , CL B:405 , HOH B:681
BINDING SITE FOR RESIDUE GOL B 403
08
AC8
SOFTWARE
LYS B:147 , ARG B:148 , HIS B:150 , ASP B:151 , HOH B:560 , HOH B:731
BINDING SITE FOR RESIDUE GOL B 404
09
AC9
SOFTWARE
ASN B:162 , HIS B:164 , SER B:246 , ILE B:247 , GLN B:248 , GOL B:403 , HOH B:506
BINDING SITE FOR RESIDUE CL B 405
10
BC1
SOFTWARE
ASN C:162 , GLN C:248 , PRO C:254 , THR C:255 , VAL C:256 , CL C:403 , HOH C:609
BINDING SITE FOR RESIDUE GOL C 401
11
BC2
SOFTWARE
LYS C:147 , ARG C:148 , HIS C:150 , ASP C:151 , HOH C:534 , HOH C:564
BINDING SITE FOR RESIDUE GOL C 402
12
BC3
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 403
13
BC4
SOFTWARE
ASN D:75 , TRP D:76 , TYR D:143 , TRP D:144 , HOH D:725 , ASP E:181 , TYR E:182 , GLN E:183 , GLN E:210 , HOH E:630
BINDING SITE FOR RESIDUE GOL D 501
14
BC5
SOFTWARE
ASN D:162 , HIS D:164 , GLN D:248 , PRO D:254 , THR D:255 , VAL D:256 , CL D:504 , HOH D:709 , HOH D:807
BINDING SITE FOR RESIDUE GOL D 502
15
BC6
SOFTWARE
LYS D:147 , ARG D:148 , HIS D:150 , ASP D:151 , HOH D:642
BINDING SITE FOR RESIDUE GOL D 503
16
BC7
SOFTWARE
HIS D:164 , SER D:246 , ILE D:247 , GLN D:248 , GOL D:502 , HOH D:611
BINDING SITE FOR RESIDUE CL D 504
17
BC8
SOFTWARE
ASN E:162 , GLN E:248 , PRO E:254 , THR E:255 , VAL E:256 , CL E:404
BINDING SITE FOR RESIDUE GOL E 401
18
BC9
SOFTWARE
GLU E:239 , ASN E:240 , ARG E:242 , ASP E:269 , GLY E:274 , LEU E:276
BINDING SITE FOR RESIDUE GOL E 402
19
CC1
SOFTWARE
LYS E:147 , ARG E:148 , HIS E:150 , ASP E:151 , HOH E:637
BINDING SITE FOR RESIDUE GOL E 403
20
CC2
SOFTWARE
ASN E:162 , HIS E:164 , SER E:246 , ILE E:247 , GOL E:401
BINDING SITE FOR RESIDUE CL E 404
21
JC3
SOFTWARE
TYR D:81 , ASP D:82 , LYS S:86 , GLY S:87 , SER S:88 , HOH S:718
BINDING SITE FOR RESIDUE GOL S 505
[
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
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)
Header - Biol.Unit 4
Biol.Unit 5 (946 KB)
Header - Biol.Unit 5
Biol.Unit 6 (938 KB)
Header - Biol.Unit 6
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4FMH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
