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2PYO
Asym. Unit
Info
Asym.Unit (252 KB)
Biol.Unit 1 (246 KB)
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(1)
Title
:
DROSOPHILA NUCLEOSOME CORE
Authors
:
C. R. Clapier, C. Petosa, C. W. Mueller
Date
:
16 May 07 (Deposition) - 06 Nov 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Nucleosome Core, Histone Fold, Structural Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. R. Clapier, S. Chakravarthy, C. Petosa, C. Fernandez-Tornero, K. Luger, C. W. Muller
Structure Of The Drosophila Nucleosome Core Particle Highlights Evolutionary Constraints On The H2A-H2B Histone Dimer.
Proteins V. 71 1 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 18)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
2m: MANGANESE (II) ION (MNm)
2n: MANGANESE (II) ION (MNn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
4
Ligand/Ion
CHLORIDE ION
2
MN
14
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DG I:48
BINDING SITE FOR RESIDUE MN I 1007
02
AC2
SOFTWARE
DG I:61
BINDING SITE FOR RESIDUE MN I 1008
03
AC3
SOFTWARE
DG I:27
BINDING SITE FOR RESIDUE MN I 1010
04
AC4
SOFTWARE
DG I:5 , DG J:-6
BINDING SITE FOR RESIDUE MN I 1011
05
AC5
SOFTWARE
DG I:-3 , DG I:-2
BINDING SITE FOR RESIDUE MN I 1012
06
AC6
SOFTWARE
DG I:-35 , DG I:-34
BINDING SITE FOR RESIDUE MN I 1013
07
AC7
SOFTWARE
DG J:61
BINDING SITE FOR RESIDUE MN J 1001
08
AC8
SOFTWARE
DT I:67 , DG J:27
BINDING SITE FOR RESIDUE MN J 1003
09
AC9
SOFTWARE
DG J:-3
BINDING SITE FOR RESIDUE MN J 1004
10
BC1
SOFTWARE
DG J:48
BINDING SITE FOR RESIDUE MN J 1005
11
BC2
SOFTWARE
DG J:-35 , DG J:-34
BINDING SITE FOR RESIDUE MN J 1009
12
BC3
SOFTWARE
DG I:-6 , DG J:5
BINDING SITE FOR RESIDUE MN J 1014
13
BC4
SOFTWARE
PRO A:121 , LYS A:122
BINDING SITE FOR RESIDUE CL A 1017
14
BC5
SOFTWARE
GLY C:45 , THR D:87 , SER D:88
BINDING SITE FOR RESIDUE CL D 1016
15
BC6
SOFTWARE
VAL D:45 , ASP E:77 , HOH E:1029
BINDING SITE FOR RESIDUE MN E 1002
16
BC7
SOFTWARE
MET E:120 , PRO E:121 , LYS E:122
BINDING SITE FOR RESIDUE CL E 1018
17
BC8
SOFTWARE
GLY G:45 , ALA G:46 , THR H:87 , SER H:88
BINDING SITE FOR RESIDUE CL H 1015
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:20-26,G:20-26)
2: HISTONE_H3_2 (A:66-74,E:66-74)
3: HISTONE_H2B (D:89-111,H:89-111)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H2A
PS00046
Histone H2A signature.
H2A_DROME
21-27
2
C:20-26
G:20-26
2
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H3_DROME
67-75
2
A:66-74
E:66-74
3
HISTONE_H2B
PS00357
Histone H2B signature.
H2B_DROME
90-112
2
D:89-111
H:89-111
[
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Exons
(0, 0)
Info
All Exons
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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
(3, 8)
Info
All SCOP Domains
1a: SCOP_d2pyoc_ (C:)
1b: SCOP_d2pyod_ (D:)
1c: SCOP_d2pyog_ (G:)
1d: SCOP_d2pyoh_ (H:)
2a: SCOP_d2pyoa_ (A:)
2b: SCOP_d2pyoe_ (E:)
3a: SCOP_d2pyob_ (B:)
3b: SCOP_d2pyof_ (F:)
View:
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Histone-fold
(277)
Superfamily
:
Histone-fold
(277)
Family
:
Nucleosome core histones
(247)
Protein domain
:
automated matches
(34)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(2)
1a
d2pyoc_
C:
1b
d2pyod_
D:
1c
d2pyog_
G:
1d
d2pyoh_
H:
Protein domain
:
Histone H3
(58)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(1)
2a
d2pyoa_
A:
2b
d2pyoe_
E:
Protein domain
:
Histone H4
(60)
Fruit fly (Drosophila melanogaster) [TaxId: 7227]
(2)
3a
d2pyob_
B:
3b
d2pyof_
F:
[
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]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2pyoA00 (A:37-135)
1b: CATH_2pyoF00 (F:15-102)
1c: CATH_2pyoC00 (C:13-120)
1d: CATH_2pyoG00 (G:11-119)
1e: CATH_2pyoB00 (B:23-102)
1f: CATH_2pyoE00 (E:37-135)
1g: CATH_2pyoD00 (D:28-122)
1h: CATH_2pyoH00 (H:28-122)
View:
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Classes
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)
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(
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Histone, subunit A
(62)
Homologous Superfamily
:
Histone, subunit A
(62)
Human (Homo sapiens)
(28)
1a
2pyoA00
A:37-135
1b
2pyoF00
F:15-102
1c
2pyoC00
C:13-120
1d
2pyoG00
G:11-119
1e
2pyoB00
B:23-102
1f
2pyoE00
E:37-135
1g
2pyoD00
D:28-122
1h
2pyoH00
H:28-122
[
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]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_2pyoG01 (G:16-89)
1b: PFAM_Histone_2pyoG02 (G:16-89)
1c: PFAM_Histone_2pyoH01 (H:28-98)
1d: PFAM_Histone_2pyoH02 (H:28-98)
1e: PFAM_Histone_2pyoE01 (E:57-131)
1f: PFAM_Histone_2pyoE02 (E:57-131)
1g: PFAM_Histone_2pyoF01 (F:24-93)
1h: PFAM_Histone_2pyoF02 (F:24-93)
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Clans
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)
(
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Families
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)
Organisms
(
)
(
)
Clan
:
Histone
(49)
Family
:
Histone
(46)
Drosophila melanogaster (Fruit fly)
(3)
1a
Histone-2pyoG01
G:16-89
1b
Histone-2pyoG02
G:16-89
1c
Histone-2pyoH01
H:28-98
1d
Histone-2pyoH02
H:28-98
1e
Histone-2pyoE01
E:57-131
1f
Histone-2pyoE02
E:57-131
1g
Histone-2pyoF01
F:24-93
1h
Histone-2pyoF02
F:24-93
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Atom Selection
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Sidechain
Hetero
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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