OCA Atlas for 3B6F

3B6F

Structural Protein Dna

date

Oct 29, 2007

title

Nucleosome Core Particle Treated With Cisplatin

authors

B.Wu, C.A.Davey

compound

source

Molecule: 147-Mer Dna
Chain: I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

Molecule: 147-Mer Dna
Chain: J
Engineered: Yes

Molecule: Histone H3.2
Chain: A, E
Synonym: Histone H3
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Molecule: Histone H2a
Chain: C, G
Synonym: Histone H2a.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1, Histone H2b.2
Engineered: Yes

symmetry

Space Group: P 21 21 21

R_factor

0.330

R_Free

0.402

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
106.327	109.380	180.585	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

3.45 Å

ligand

enzyme

Gene
Ontology

Chain	Function	Process	Component
A, E
C, G
F, B
H, D

Primary reference

Site selectivity of platinum anticancer therapeutics., Wu B, Droge P, Davey CA, Nat Chem Biol. 2008 Feb;4(2):110-2. Epub 2007 Dec 23. PMID:18157123

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (246 Kb) [Save to disk]

Biological Unit Coordinates (3b6f.pdb1.gz) 239 Kb

LPC: Ligand-Protein Contacts for 3B6F

CSU: Contacts of Structural Units for 3B6F

Likely Quarternary Molecular Structure file(s) for 3B6F

Structure Factors (222 Kb)

Retrieve 3B6F in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3B6F from S2C, [Save to disk]

Re-refined 3b6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3B6F in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3B6F

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3B6F, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3b6f_G] [3b6f_A] [3b6f] [3b6f_E] [3b6f_J] [3b6f_H] [3b6f_B] [3b6f_I] [3b6f_F] [3b6f_D] [3b6f_C]

SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]

Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM

Domains found in 3B6F: [H2A] [H2B] [H3] [H4 ] by SMART

Other resources with information on 3B6F

Community annotation for 3B6F at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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