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1M3Y
Biol. Unit 3
Info
Asym.Unit (269 KB)
Biol.Unit 1 (199 KB)
Biol.Unit 2 (198 KB)
Biol.Unit 3 (197 KB)
Biol.Unit 4 (197 KB)
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(1)
Title
:
THE STRUCTURE OF 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
:
01 Jul 02 (Deposition) - 04 Dec 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (3x)
Biol. Unit 2: B (3x)
Biol. Unit 3: C (3x)
Biol. Unit 4: D (3x)
Keywords
:
Major Capsit Protein Vp54, Pbcv-1, Chlorella Virus, Jelly Roll Motif, Glycoprotein, 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
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Hetero Components
(3, 15)
Info
All Hetero Components
1a: MERCURY (II) ION (HGa)
1b: MERCURY (II) ION (HGb)
1c: MERCURY (II) ION (HGc)
1d: MERCURY (II) ION (HGd)
1e: MERCURY (II) ION (HGe)
1f: MERCURY (II) ION (HGf)
1g: MERCURY (II) ION (HGg)
1h: MERCURY (II) ION (HGh)
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)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
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)
4e: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGe)
4f: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGf)
4g: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGg)
4h: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HG
-1
Ligand/Ion
MERCURY (II) ION
2
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
6
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
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Sites
(7, 7)
Info
All Sites
1: BC2 (SOFTWARE)
2: BC3 (SOFTWARE)
3: BC4 (SOFTWARE)
4: BC5 (SOFTWARE)
5: BC6 (SOFTWARE)
6: CC7 (SOFTWARE)
7: CC8 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
BC2
SOFTWARE
ASN C:280 , GLY C:289 , THR C:290 , ALA C:293 , THR C:391 , PRO C:393 , MAN C:639 , HOH C:648
BINDING SITE FOR RESIDUE NDG C 638
2
BC3
SOFTWARE
ALA C:291 , NDG C:638
BINDING SITE FOR RESIDUE MAN C 639
3
BC4
SOFTWARE
SER C:387 , ILE C:388 , ASP C:389 , ALA C:395 , GLY C:398 , ASN C:399 , MAN C:641
BINDING SITE FOR RESIDUE NAG C 640
4
BC5
SOFTWARE
NAG C:640
BINDING SITE FOR RESIDUE MAN C 641
5
BC6
SOFTWARE
ASP C:389 , THR C:391 , ASN C:406 , THR C:409
BINDING SITE FOR RESIDUE NDG C 642
6
CC7
SOFTWARE
LEU C:320 , CYS C:369 , ILE C:374
BINDING SITE FOR RESIDUE HG C 643
7
CC8
SOFTWARE
SER C:242 , CYS C:386 , ASN C:406 , THR C:409
BINDING SITE FOR RESIDUE HG C 644
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1m3ya1 (A:25-221)
1b: SCOP_d1m3ya2 (A:222-437)
1c: SCOP_d1m3yb1 (B:25-221)
1d: SCOP_d1m3yb2 (B:222-437)
1e: SCOP_d1m3yc1 (C:25-221)
1f: SCOP_d1m3yc2 (C:222-437)
1g: SCOP_d1m3yd1 (D:25-221)
1h: SCOP_d1m3yd2 (D:222-437)
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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
d1m3ya1
A:25-221
1b
d1m3ya2
A:222-437
1c
d1m3yb1
B:25-221
1d
d1m3yb2
B:222-437
1e
d1m3yc1
C:25-221
1f
d1m3yc2
C:222-437
1g
d1m3yd1
D:25-221
1h
d1m3yd2
D:222-437
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1m3yA01 (A:35-222)
1b: CATH_1m3yB01 (B:35-222)
1c: CATH_1m3yC01 (C:35-222)
1d: CATH_1m3yD01 (D:35-222)
2a: CATH_1m3yA02 (A:223-437)
2b: CATH_1m3yB02 (B:223-437)
2c: CATH_1m3yC02 (C:223-437)
2d: CATH_1m3yD02 (D:223-437)
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)
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
1m3yA01
A:35-222
1b
1m3yB01
B:35-222
1c
1m3yC01
C:35-222
1d
1m3yD01
D:35-222
Homologous Superfamily
:
Major capsid protein Vp54
(2)
Paramecium bursaria chlorella virus 1. Organism_taxid: 10506.
(1)
2a
1m3yA02
A:223-437
2b
1m3yB02
B:223-437
2c
1m3yC02
C:223-437
2d
1m3yD02
D:223-437
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Capsid_NCLDV_1m3yD01 (D:196-433)
1b: PFAM_Capsid_NCLDV_1m3yD02 (D:196-433)
1c: PFAM_Capsid_NCLDV_1m3yD03 (D:196-433)
1d: PFAM_Capsid_NCLDV_1m3yD04 (D:196-433)
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Clans
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)
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)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Capsid_NCLDV]
(2)
Family
:
Capsid_NCLDV
(2)
Paramecium bursaria Chlorella virus 1 (PBCV-1)
(2)
1a
Capsid_NCLDV-1m3yD01
D:196-433
1b
Capsid_NCLDV-1m3yD02
D:196-433
1c
Capsid_NCLDV-1m3yD03
D:196-433
1d
Capsid_NCLDV-1m3yD04
D:196-433
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Asym.Unit (269 KB)
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Biol.Unit 1 (199 KB)
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Biol.Unit 3 (197 KB)
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