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1KX3
Asym. Unit
Info
Asym.Unit (270 KB)
Biol.Unit 1 (263 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE, NCP146, AT 2.0 A RESOLUTION
Authors
:
C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, T. J. Richmond
Date
:
31 Jan 02 (Deposition) - 25 Dec 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
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, Chromatin, Histone, Protein-Dna Interaction, Nucleoprotein, Supercoiled Dna, Nucleosome Core, Protein- Dna Complex, Structural Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. A. Davey, D. F. Sargent, K. Luger, A. W. Maeder, T. J. Richmond
Solvent Mediated Interactions In The Structure Of The Nucleosome Core Particle At 1. 9 A Resolution
J. Mol. Biol. V. 319 1097 2002
(for further references see the
PDB file header
)
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Hetero Components
(1, 13)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
1i: MANGANESE (II) ION (MNi)
1j: MANGANESE (II) ION (MNj)
1k: MANGANESE (II) ION (MNk)
1l: MANGANESE (II) ION (MNl)
1m: MANGANESE (II) ION (MNm)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MN
13
Ligand/Ion
MANGANESE (II) ION
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Sites
(13, 13)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
DG I:-34 , DG I:-33 , HOH I:1031
BINDING SITE FOR RESIDUE MN I 944
02
AC2
SOFTWARE
DG J:60 , HOH J:1032
BINDING SITE FOR RESIDUE MN J 945
03
AC3
SOFTWARE
VAL D:45 , ASP E:77 , HOH E:999 , HOH E:1020 , HOH E:1032 , HOH F:155
BINDING SITE FOR RESIDUE MN E 946
04
AC4
SOFTWARE
DT I:67 , DG J:26 , HOH J:1021
BINDING SITE FOR RESIDUE MN J 947
05
AC5
SOFTWARE
DG J:-3
BINDING SITE FOR RESIDUE MN J 948
06
AC6
SOFTWARE
DG J:47 , HOH J:1023
BINDING SITE FOR RESIDUE MN J 949
07
AC7
SOFTWARE
HOH J:983 , HOH J:1024 , HOH J:1060
BINDING SITE FOR RESIDUE MN I 950
08
AC8
SOFTWARE
DG I:48
BINDING SITE FOR RESIDUE MN I 951
09
AC9
SOFTWARE
DG I:61 , HOH I:962 , HOH I:990 , HOH I:1060
BINDING SITE FOR RESIDUE MN I 952
10
BC1
SOFTWARE
DG J:-34 , DG J:-35 , HOH J:1027 , HOH J:1059
BINDING SITE FOR RESIDUE MN J 953
11
BC2
SOFTWARE
DG J:7
BINDING SITE FOR RESIDUE MN J 954
12
BC3
SOFTWARE
DG I:27 , HOH I:1061 , HOH I:1079
BINDING SITE FOR RESIDUE MN I 955
13
BC4
SOFTWARE
DG I:65 , HOH I:958
BINDING SITE FOR RESIDUE MN I 956
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(3, 6)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H2A (C:21-27,G:21-27)
2: HISTONE_H3_2 (A:66-74,E:66-74)
3: HISTONE_H2B (D:89-111,H:89-111)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H2A
PS00046
Histone H2A signature.
H2A1_XENLA
22-28
2
C:21-27
G:21-27
2
HISTONE_H3_2
PS00959
Histone H3 signature 2.
H32_XENLA
67-75
2
A:66-74
E:66-74
3
HISTONE_H2B
PS00357
Histone H2B signature.
H2B11_XENLA
93-115
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.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1kx3c_ (C:)
1b: SCOP_d1kx3g_ (G:)
2a: SCOP_d1kx3d_ (D:)
2b: SCOP_d1kx3h_ (H:)
3a: SCOP_d1kx3a_ (A:)
3b: SCOP_d1kx3e_ (E:)
4a: SCOP_d1kx3b_ (B:)
4b: SCOP_d1kx3f_ (F:)
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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
:
Histone H2A
(45)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(34)
1a
d1kx3c_
C:
1b
d1kx3g_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d1kx3d_
D:
2b
d1kx3h_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d1kx3a_
A:
3b
d1kx3e_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d1kx3b_
B:
4b
d1kx3f_
F:
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1kx3A00 (A:38-135)
1b: CATH_1kx3G00 (G:14-119)
1c: CATH_1kx3C00 (C:14-120)
1d: CATH_1kx3D00 (D:29-122)
1e: CATH_1kx3H00 (H:29-122)
1f: CATH_1kx3E00 (E:38-135)
1g: CATH_1kx3F00 (F:16-102)
1h: CATH_1kx3B00 (B:21-102)
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)
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
1kx3A00
A:38-135
1b
1kx3G00
G:14-119
1c
1kx3C00
C:14-120
1d
1kx3D00
D:29-122
1e
1kx3H00
H:29-122
1f
1kx3E00
E:38-135
1g
1kx3F00
F:16-102
1h
1kx3B00
B:21-102
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Asym.Unit (270 KB)
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