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2PYO
Biol. Unit 1
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
(0, 0)
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)
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Sorry, no Info available
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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:
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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 only available for the asymmetric unit)
All SNPs/Variants
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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)
;
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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
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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
(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:)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
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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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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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Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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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
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select residue range 5 to 10 in chain 'A'
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