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.
PLEASE WAIT...
Getting 'Exon' information from database.
1J5Q
Asym. Unit
Info
Asym.Unit (150 KB)
Biol.Unit 1 (414 KB)
Biol.Unit 2 (209 KB)
Biol.Unit 3 (210 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE AND EVOLUTION OF THE MAJOR CAPSID PROTEIN OF A LARGE, LIPID-CONTAINING, DNA VIRUS.
Authors
:
N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Gra J. L. Van Etten, M. G. Rossmann
Date
:
27 Jun 02 (Deposition) - 20 Nov 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Biol. Unit 2: A (3x)
Biol. Unit 3: B (3x)
Keywords
:
Pbcv-1, Major Capsid Protein Of Large Dna Virus, Vp54, Chlorella Virus, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten, M. G. Rossmann
The Structure And Evolution Of The Major Capsid Protein Of Large, Lipid-Containing Dna Virus
Proc. Natl. Acad. Sci. Usa V. 99 14758 2002
[
close entry info
]
Hetero Components
(4, 38)
Info
All Hetero Components
1a: MERCURY (II) ION (HGa)
1b: MERCURY (II) ION (HGb)
1c: MERCURY (II) ION (HGc)
1d: MERCURY (II) ION (HGd)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
2g: ALPHA-D-MANNOSE (MANg)
2h: ALPHA-D-MANNOSE (MANh)
2i: ALPHA-D-MANNOSE (MANi)
2j: ALPHA-D-MANNOSE (MANj)
2k: ALPHA-D-MANNOSE (MANk)
2l: ALPHA-D-MANNOSE (MANl)
2m: ALPHA-D-MANNOSE (MANm)
2n: ALPHA-D-MANNOSE (MANn)
2o: ALPHA-D-MANNOSE (MANo)
2p: ALPHA-D-MANNOSE (MANp)
2q: ALPHA-D-MANNOSE (MANq)
2r: ALPHA-D-MANNOSE (MANr)
2s: ALPHA-D-MANNOSE (MANs)
2t: ALPHA-D-MANNOSE (MANt)
2u: ALPHA-D-MANNOSE (MANu)
2v: ALPHA-D-MANNOSE (MANv)
2w: ALPHA-D-MANNOSE (MANw)
2x: ALPHA-D-MANNOSE (MANx)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
4c: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGc)
4d: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HG
4
Ligand/Ion
MERCURY (II) ION
2
MAN
24
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
4
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(38, 38)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:280 , GLY A:289 , THR A:290 , ALA A:293 , PRO A:393 , MAN A:439 , MAN A:440 , MAN A:441 , MAN A:452
BINDING SITE FOR RESIDUE NAG A 438
02
AC2
SOFTWARE
THR A:391 , NAG A:438 , MAN A:441 , MAN A:442 , NAG A:450
BINDING SITE FOR RESIDUE MAN A 439
03
AC3
SOFTWARE
NAG A:438 , MAN A:441 , MAN A:442
BINDING SITE FOR RESIDUE MAN A 440
04
AC4
SOFTWARE
NAG A:438 , MAN A:439 , MAN A:440 , MAN A:442
BINDING SITE FOR RESIDUE MAN A 441
05
AC5
SOFTWARE
MAN A:439 , MAN A:440 , MAN A:441
BINDING SITE FOR RESIDUE MAN A 442
06
AC6
SOFTWARE
ASN A:81 , GLY A:82 , ASN A:138 , LEU A:140 , NAG A:444 , MAN A:445 , MAN A:447 , MAN A:448 , MAN A:452
BINDING SITE FOR RESIDUE MAN A 443
07
AC7
SOFTWARE
GLY A:287 , ASP A:299 , MAN A:443 , NDG A:446 , MAN A:447 , MAN A:448
BINDING SITE FOR RESIDUE NAG A 444
08
AC8
SOFTWARE
MAN A:443 , MAN A:447 , MAN A:448 , MAN A:452
BINDING SITE FOR RESIDUE MAN A 445
09
AC9
SOFTWARE
GLY A:83 , ASP A:299 , ASN A:302 , NAG A:444
BINDING SITE FOR RESIDUE NDG A 446
10
BC1
SOFTWARE
MAN A:443 , NAG A:444 , MAN A:445 , MAN A:448
BINDING SITE FOR RESIDUE MAN A 447
11
BC2
SOFTWARE
MAN A:443 , NAG A:444 , MAN A:445 , MAN A:447
BINDING SITE FOR RESIDUE MAN A 448
12
BC3
SOFTWARE
ILE A:388 , ASP A:389 , ALA A:395 , GLY A:398 , ASN A:399 , MAN A:453 , MAN A:454
BINDING SITE FOR RESIDUE NDG A 449
13
BC4
SOFTWARE
ASP A:389 , THR A:391 , ASN A:406 , MAN A:439 , MAN A:451
BINDING SITE FOR RESIDUE NAG A 450
14
BC5
SOFTWARE
NAG A:450
BINDING SITE FOR RESIDUE MAN A 451
15
BC6
SOFTWARE
NAG A:438 , MAN A:443 , MAN A:445
BINDING SITE FOR RESIDUE MAN A 452
16
BC7
SOFTWARE
VAL A:141 , ALA A:394 , NDG A:449
BINDING SITE FOR RESIDUE MAN A 453
17
BC8
SOFTWARE
NDG A:449
BINDING SITE FOR RESIDUE MAN A 454
18
BC9
SOFTWARE
ASN B:280 , GLY B:289 , THR B:290 , ALA B:293 , THR B:391 , MAN B:539 , MAN B:540 , MAN B:541 , MAN B:552
BINDING SITE FOR RESIDUE NAG B 538
19
CC1
SOFTWARE
NAG B:538 , MAN B:541 , MAN B:542 , NDG B:550
BINDING SITE FOR RESIDUE MAN B 539
20
CC2
SOFTWARE
NAG B:538 , MAN B:541
BINDING SITE FOR RESIDUE MAN B 540
21
CC3
SOFTWARE
ALA B:291 , NAG B:538 , MAN B:539 , MAN B:540 , MAN B:542
BINDING SITE FOR RESIDUE MAN B 541
22
CC4
SOFTWARE
MAN B:539 , MAN B:541
BINDING SITE FOR RESIDUE MAN B 542
23
CC5
SOFTWARE
ASN B:81 , GLY B:82 , ASN B:138 , LEU B:140 , NDG B:544 , MAN B:545 , MAN B:547 , MAN B:552
BINDING SITE FOR RESIDUE MAN B 543
24
CC6
SOFTWARE
GLY B:82 , MAN B:543 , NAG B:546 , MAN B:547
BINDING SITE FOR RESIDUE NDG B 544
25
CC7
SOFTWARE
MAN B:543 , MAN B:548 , MAN B:552
BINDING SITE FOR RESIDUE MAN B 545
26
CC8
SOFTWARE
ASP B:299 , ASN B:302 , NDG B:544
BINDING SITE FOR RESIDUE NAG B 546
27
CC9
SOFTWARE
MAN B:543 , NDG B:544 , MAN B:548
BINDING SITE FOR RESIDUE MAN B 547
28
DC1
SOFTWARE
ALA B:292 , MAN B:545 , MAN B:547
BINDING SITE FOR RESIDUE MAN B 548
29
DC2
SOFTWARE
SER B:387 , ILE B:388 , ASP B:389 , ALA B:395 , GLY B:398 , ASN B:399 , MAN B:553 , MAN B:554
BINDING SITE FOR RESIDUE NAG B 549
30
DC3
SOFTWARE
ASP B:389 , ALA B:390 , ASN B:406 , MAN B:539 , MAN B:551
BINDING SITE FOR RESIDUE NDG B 550
31
DC4
SOFTWARE
NDG B:550
BINDING SITE FOR RESIDUE MAN B 551
32
DC5
SOFTWARE
NAG B:538 , MAN B:543 , MAN B:545
BINDING SITE FOR RESIDUE MAN B 552
33
DC6
SOFTWARE
VAL B:141 , ALA B:394 , GLY B:398 , NAG B:549
BINDING SITE FOR RESIDUE MAN B 553
34
DC7
SOFTWARE
NAG B:549
BINDING SITE FOR RESIDUE MAN B 554
35
DC8
SOFTWARE
LEU A:320 , CYS A:369 , PHE A:371 , ILE A:374
BINDING SITE FOR RESIDUE HG A 455
36
DC9
SOFTWARE
CYS A:386 , THR A:409
BINDING SITE FOR RESIDUE HG A 456
37
EC1
SOFTWARE
CYS B:386 , ASN B:406 , THR B:409
BINDING SITE FOR RESIDUE HG B 457
38
EC2
SOFTWARE
LEU B:320 , PHE B:356 , CYS B:369 , PHE B:371 , ILE B:374
BINDING SITE FOR RESIDUE HG B 458
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1j5qa1 (A:25-221)
1b: SCOP_d1j5qb1 (B:25-221)
1c: SCOP_d1j5qb2 (B:222-437)
1d: SCOP_d1j5qa2 (A:222-437)
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 II dsDNA viruses VP
(10)
Family
:
Major capsid protein vp54
(2)
Protein domain
:
Major capsid protein vp54
(2)
Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506]
(2)
1a
d1j5qa1
A:25-221
1b
d1j5qb1
B:25-221
1c
d1j5qb2
B:222-437
1d
d1j5qa2
A:222-437
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1j5qA01 (A:25-222)
1b: CATH_1j5qB01 (B:25-222)
2a: CATH_1j5qA02 (A:223-437)
2b: CATH_1j5qB02 (B:223-437)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Adenovirus Type 2 Hexon; domain 4
(7)
Homologous Superfamily
:
Adenovirus Type 2 Hexon, domain 4
(4)
Paramecium bursaria chlorella virus 1. Organism_taxid: 10506
(1)
1a
1j5qA01
A:25-222
1b
1j5qB01
B:25-222
Homologous Superfamily
:
Major capsid protein Vp54
(2)
Paramecium bursaria chlorella virus 1. Organism_taxid: 10506
(1)
2a
1j5qA02
A:223-437
2b
1j5qB02
B:223-437
[
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
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 (150 KB)
Header - Asym.Unit
Biol.Unit 1 (414 KB)
Header - Biol.Unit 1
Biol.Unit 2 (209 KB)
Header - Biol.Unit 2
Biol.Unit 3 (210 KB)
Header - Biol.Unit 3
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
1J5Q
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
