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3KIC
Biol. Unit 1
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Asym.Unit (1.7 MB)
Biol.Unit 1, α-C (4.9 MB)
Biol.Unit 1 (4.9 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ADENO-ASSOCIATED VIRUS SEROTYPE 3B
Authors
:
T. F. Lerch, Q. Xie, M. S. Chapman
Date
:
01 Nov 09 (Deposition) - 28 Apr 10 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T (3x)
Keywords
:
Virus, Capsid, Parvovirus, Icosahedral Virus, Beta Barrel, Single- Stranded, Dependovirus
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. F. Lerch, Q. Xie, M. S. Chapman
The Structure Of Adeno-Associated Virus Serotype 3B (Aav-3B): Insights Into Receptor Binding And Immune Evasion
Virology V. 403 26 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 60)
Info
All Hetero Components
1a: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Ma)
1b: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mb)
1c: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mc)
1d: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Md)
1e: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Me)
1f: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mf)
1g: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mg)
1h: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mh)
1i: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mi)
1j: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mj)
1k: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mk)
1l: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Ml)
1m: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mm)
1n: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mn)
1o: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mo)
1p: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mp)
1q: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mq)
1r: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mr)
1s: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Ms)
1t: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (D5Mt)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D5M
60
Ligand/Ion
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:418 , HIS A:630 , GLY A:639
BINDING SITE FOR RESIDUE D5M A 999
02
AC2
SOFTWARE
VAL B:418 , HIS B:630 , GLY B:639
BINDING SITE FOR RESIDUE D5M B 999
03
AC3
SOFTWARE
VAL C:418 , HIS C:630 , GLY C:639
BINDING SITE FOR RESIDUE D5M C 999
04
AC4
SOFTWARE
VAL D:418 , HIS D:630 , GLY D:639
BINDING SITE FOR RESIDUE D5M D 999
05
AC5
SOFTWARE
VAL E:418 , HIS E:630 , GLY E:639
BINDING SITE FOR RESIDUE D5M E 999
06
AC6
SOFTWARE
VAL F:418 , HIS F:630 , GLY F:639
BINDING SITE FOR RESIDUE D5M F 999
07
AC7
SOFTWARE
VAL G:418 , HIS G:630 , GLY G:639
BINDING SITE FOR RESIDUE D5M G 999
08
AC8
SOFTWARE
VAL H:418 , HIS H:630 , GLY H:639
BINDING SITE FOR RESIDUE D5M H 999
09
AC9
SOFTWARE
VAL I:418 , HIS I:630 , GLY I:639
BINDING SITE FOR RESIDUE D5M I 999
10
BC1
SOFTWARE
VAL J:418 , HIS J:630 , GLY J:639
BINDING SITE FOR RESIDUE D5M J 999
11
BC2
SOFTWARE
VAL K:418 , HIS K:630 , GLY K:639
BINDING SITE FOR RESIDUE D5M K 999
12
BC3
SOFTWARE
VAL L:418 , HIS L:630 , GLY L:639
BINDING SITE FOR RESIDUE D5M L 999
13
BC4
SOFTWARE
VAL M:418 , HIS M:630 , GLY M:639
BINDING SITE FOR RESIDUE D5M M 999
14
BC5
SOFTWARE
VAL N:418 , HIS N:630 , GLY N:639
BINDING SITE FOR RESIDUE D5M N 999
15
BC6
SOFTWARE
VAL O:418 , HIS O:630 , GLY O:639
BINDING SITE FOR RESIDUE D5M O 999
16
BC7
SOFTWARE
VAL P:418 , HIS P:630 , GLY P:639
BINDING SITE FOR RESIDUE D5M P 999
17
BC8
SOFTWARE
VAL Q:418 , HIS Q:630 , GLY Q:639
BINDING SITE FOR RESIDUE D5M Q 999
18
BC9
SOFTWARE
VAL R:418 , HIS R:630 , GLY R:639
BINDING SITE FOR RESIDUE D5M R 999
19
CC1
SOFTWARE
VAL S:418 , HIS S:630 , GLY S:639
BINDING SITE FOR RESIDUE D5M S 999
20
CC2
SOFTWARE
VAL T:418 , HIS T:630 , GLY T:639
BINDING SITE FOR RESIDUE D5M T 999
[
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]
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
[
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]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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_d3kica_ (A:)
1b: SCOP_d3kicb_ (B:)
1c: SCOP_d3kick_ (K:)
1d: SCOP_d3kicl_ (L:)
1e: SCOP_d3kicm_ (M:)
1f: SCOP_d3kicn_ (N:)
1g: SCOP_d3kico_ (O:)
1h: SCOP_d3kicp_ (P:)
1i: SCOP_d3kicq_ (Q:)
1j: SCOP_d3kicr_ (R:)
1k: SCOP_d3kics_ (S:)
1l: SCOP_d3kict_ (T:)
1m: SCOP_d3kicc_ (C:)
1n: SCOP_d3kicd_ (D:)
1o: SCOP_d3kice_ (E:)
1p: SCOP_d3kicf_ (F:)
1q: SCOP_d3kicg_ (G:)
1r: SCOP_d3kich_ (H:)
1s: SCOP_d3kici_ (I:)
1t: SCOP_d3kicj_ (J:)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Nucleoplasmin-like/VP (viral coat and capsid proteins)
(278)
Superfamily
:
ssDNA viruses
(39)
Family
:
Parvoviridae-like VP
(31)
Protein domain
:
automated matches
(15)
Adeno-associated virus 3b [TaxId: 68742]
(2)
1a
d3kica_
A:
1b
d3kicb_
B:
1c
d3kick_
K:
1d
d3kicl_
L:
1e
d3kicm_
M:
1f
d3kicn_
N:
1g
d3kico_
O:
1h
d3kicp_
P:
1i
d3kicq_
Q:
1j
d3kicr_
R:
1k
d3kics_
S:
1l
d3kict_
T:
1m
d3kicc_
C:
1n
d3kicd_
D:
1o
d3kice_
E:
1p
d3kicf_
F:
1q
d3kicg_
G:
1r
d3kich_
H:
1s
d3kici_
I:
1t
d3kicj_
J:
[
close SCOP info
]
CATH Domains
(1, 20)
Info
all CATH domains
1a: CATH_3kicA00 (A:217-736)
1b: CATH_3kicB00 (B:217-736)
1c: CATH_3kicK00 (K:217-736)
1d: CATH_3kicL00 (L:217-736)
1e: CATH_3kicM00 (M:217-736)
1f: CATH_3kicN00 (N:217-736)
1g: CATH_3kicO00 (O:217-736)
1h: CATH_3kicP00 (P:217-736)
1i: CATH_3kicQ00 (Q:217-736)
1j: CATH_3kicR00 (R:217-736)
1k: CATH_3kicS00 (S:217-736)
1l: CATH_3kicT00 (T:217-736)
1m: CATH_3kicC00 (C:217-736)
1n: CATH_3kicD00 (D:217-736)
1o: CATH_3kicE00 (E:217-736)
1p: CATH_3kicF00 (F:217-736)
1q: CATH_3kicG00 (G:217-736)
1r: CATH_3kicH00 (H:217-736)
1s: CATH_3kicI00 (I:217-736)
1t: CATH_3kicJ00 (J:217-736)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Empty Capsid Viral Protein 2
(22)
Homologous Superfamily
:
Empty Capsid Viral Protein 2
(22)
Adeno-associated virus 3b. Organism_taxid: 68742.
(2)
1a
3kicA00
A:217-736
1b
3kicB00
B:217-736
1c
3kicK00
K:217-736
1d
3kicL00
L:217-736
1e
3kicM00
M:217-736
1f
3kicN00
N:217-736
1g
3kicO00
O:217-736
1h
3kicP00
P:217-736
1i
3kicQ00
Q:217-736
1j
3kicR00
R:217-736
1k
3kicS00
S:217-736
1l
3kicT00
T:217-736
1m
3kicC00
C:217-736
1n
3kicD00
D:217-736
1o
3kicE00
E:217-736
1p
3kicF00
F:217-736
1q
3kicG00
G:217-736
1r
3kicH00
H:217-736
1s
3kicI00
I:217-736
1t
3kicJ00
J:217-736
[
close CATH info
]
Pfam Domains
(1, 20)
Info
all PFAM domains
1a: PFAM_Parvo_coat_3kicT01 (T:217-714)
1b: PFAM_Parvo_coat_3kicT02 (T:217-714)
1c: PFAM_Parvo_coat_3kicT03 (T:217-714)
1d: PFAM_Parvo_coat_3kicT04 (T:217-714)
1e: PFAM_Parvo_coat_3kicT05 (T:217-714)
1f: PFAM_Parvo_coat_3kicT06 (T:217-714)
1g: PFAM_Parvo_coat_3kicT07 (T:217-714)
1h: PFAM_Parvo_coat_3kicT08 (T:217-714)
1i: PFAM_Parvo_coat_3kicT09 (T:217-714)
1j: PFAM_Parvo_coat_3kicT10 (T:217-714)
1k: PFAM_Parvo_coat_3kicT11 (T:217-714)
1l: PFAM_Parvo_coat_3kicT12 (T:217-714)
1m: PFAM_Parvo_coat_3kicT13 (T:217-714)
1n: PFAM_Parvo_coat_3kicT14 (T:217-714)
1o: PFAM_Parvo_coat_3kicT15 (T:217-714)
1p: PFAM_Parvo_coat_3kicT16 (T:217-714)
1q: PFAM_Parvo_coat_3kicT17 (T:217-714)
1r: PFAM_Parvo_coat_3kicT18 (T:217-714)
1s: PFAM_Parvo_coat_3kicT19 (T:217-714)
1t: PFAM_Parvo_coat_3kicT20 (T:217-714)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Parvo_coat]
(8)
Family
:
Parvo_coat
(8)
Adeno-associated virus 3B
(2)
1a
Parvo_coat-3kicT01
T:217-714
1b
Parvo_coat-3kicT02
T:217-714
1c
Parvo_coat-3kicT03
T:217-714
1d
Parvo_coat-3kicT04
T:217-714
1e
Parvo_coat-3kicT05
T:217-714
1f
Parvo_coat-3kicT06
T:217-714
1g
Parvo_coat-3kicT07
T:217-714
1h
Parvo_coat-3kicT08
T:217-714
1i
Parvo_coat-3kicT09
T:217-714
1j
Parvo_coat-3kicT10
T:217-714
1k
Parvo_coat-3kicT11
T:217-714
1l
Parvo_coat-3kicT12
T:217-714
1m
Parvo_coat-3kicT13
T:217-714
1n
Parvo_coat-3kicT14
T:217-714
1o
Parvo_coat-3kicT15
T:217-714
1p
Parvo_coat-3kicT16
T:217-714
1q
Parvo_coat-3kicT17
T:217-714
1r
Parvo_coat-3kicT18
T:217-714
1s
Parvo_coat-3kicT19
T:217-714
1t
Parvo_coat-3kicT20
T:217-714
[
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