PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2NZD
Asym. Unit
Info
Asym.Unit (249 KB)
Biol.Unit 1 (242 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
NUCLEOSOME CORE PARTICLE CONTAINING 145 BP OF DNA
Authors
:
M. S. Ong, T. J. Richmond, C. A. Davey
Date
:
23 Nov 06 (Deposition) - 10 Apr 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
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, Dna Stretching, Dna Kinking, Double-Helix, Structural Protein/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. S. Ong, T. J. Richmond, C. A. Davey
Dna Stretching And Extreme Kinking In The Nucleosome Core
J. Mol. Biol. V. 368 1067 2007
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 11)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
11
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL D:45 , ASP E:77 , HOH E:1008 , HOH E:1010 , HOH E:1012 , HOH F:117
BINDING SITE FOR RESIDUE MN E 1001
02
AC2
SOFTWARE
DG I:-34 , DG I:-33
BINDING SITE FOR RESIDUE MN I 1003
03
AC3
SOFTWARE
DG J:60 , DG J:61
BINDING SITE FOR RESIDUE MN J 1004
04
AC4
SOFTWARE
DG J:26
BINDING SITE FOR RESIDUE MN J 1005
05
AC5
SOFTWARE
DG J:4
BINDING SITE FOR RESIDUE MN J 1006
06
AC6
SOFTWARE
DG J:47 , HOH J:1015 , HOH J:1019
BINDING SITE FOR RESIDUE MN J 1007
07
AC7
SOFTWARE
DG I:47
BINDING SITE FOR RESIDUE MN I 1008
08
AC8
SOFTWARE
DG I:60 , HOH I:1013
BINDING SITE FOR RESIDUE MN I 1009
09
AC9
SOFTWARE
DG J:-34 , DG J:-33 , HOH J:1012
BINDING SITE FOR RESIDUE MN J 1010
10
BC1
SOFTWARE
DA I:25 , DG I:26
BINDING SITE FOR RESIDUE MN I 1011
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
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:
Select:
Label:
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
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
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.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d2nzdc_ (C:)
1b: SCOP_d2nzdg_ (G:)
2a: SCOP_d2nzdd_ (D:)
2b: SCOP_d2nzdh_ (H:)
3a: SCOP_d2nzda_ (A:)
3b: SCOP_d2nzde_ (E:)
4a: SCOP_d2nzdb_ (B:)
4b: SCOP_d2nzdf_ (F:)
View:
Select:
Label:
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
:
Histone H2A
(45)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(34)
1a
d2nzdc_
C:
1b
d2nzdg_
G:
Protein domain
:
Histone H2B
(48)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(35)
2a
d2nzdd_
D:
2b
d2nzdh_
H:
Protein domain
:
Histone H3
(58)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(39)
3a
d2nzda_
A:
3b
d2nzde_
E:
Protein domain
:
Histone H4
(60)
African clawed frog (Xenopus laevis) [TaxId: 8355]
(38)
4a
d2nzdb_
B:
4b
d2nzdf_
F:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2nzdA00 (A:38-134)
1b: CATH_2nzdD00 (D:28-122)
1c: CATH_2nzdH00 (H:28-122)
1d: CATH_2nzdF00 (F:16-102)
1e: CATH_2nzdB00 (B:21-102)
1f: CATH_2nzdC00 (C:14-119)
1g: CATH_2nzdG00 (G:14-119)
1h: CATH_2nzdE00 (E:38-134)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Histone, subunit A
(62)
Homologous Superfamily
:
Histone, subunit A
(62)
[unclassified]
(10)
1a
2nzdA00
A:38-134
1b
2nzdD00
D:28-122
1c
2nzdH00
H:28-122
1d
2nzdF00
F:16-102
1e
2nzdB00
B:21-102
1f
2nzdC00
C:14-119
1g
2nzdG00
G:14-119
1h
2nzdE00
E:38-134
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Histone_2nzdG01 (G:17-90)
1b: PFAM_Histone_2nzdG02 (G:17-90)
1c: PFAM_Histone_2nzdH01 (H:28-98)
1d: PFAM_Histone_2nzdH02 (H:28-98)
1e: PFAM_Histone_2nzdE01 (E:57-131)
1f: PFAM_Histone_2nzdE02 (E:57-131)
1g: PFAM_Histone_2nzdF01 (F:24-93)
1h: PFAM_Histone_2nzdF02 (F:24-93)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Histone
(49)
Family
:
Histone
(46)
Xenopus laevis (African clawed frog)
(32)
1a
Histone-2nzdG01
G:17-90
1b
Histone-2nzdG02
G:17-90
1c
Histone-2nzdH01
H:28-98
1d
Histone-2nzdH02
H:28-98
1e
Histone-2nzdE01
E:57-131
1f
Histone-2nzdE02
E:57-131
1g
Histone-2nzdF01
F:24-93
1h
Histone-2nzdF02
F:24-93
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (249 KB)
Header - Asym.Unit
Biol.Unit 1 (242 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2NZD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help