5XF3 Structural Protein Dna date Apr 07, 2017
title Nucleosome Core Particle With An Adduct Of A Binuclear Rapta Arene-Phosphaadamantane) Compound Having A 1,2- Diphenylethylenediamine Linker (R,R-Configuration)
authors Z.Ma, Z.Adhireksan, B.S.Murray, P.J.Dyson, C.A.Davey
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a,Histone H3b,Histone H3c,Histone H3 H3f,Histone H3h,Histone H3i,Histone H3j,Histone H3k,Hi H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h3a, H3fa, Hist1h3b, H3fl, Hist1h3c, H3fc, Hist1 H3fb, Hist1h3e, H3fd, Hist1h3f, H3fi, Hist1h3g, H3fh, Hist1 H3fk, Hist1h3i, H3ff, Hist1h3j, H3fj;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h4a, H4a, H4fa, Hist1h4b, H4i, H4fi, Hist1h4c, H4fg, Hist1h4d, H4b, H4fb, Hist1h4e, H4j, H4fj, Hist1h4f, H4fc, Hist1h4h, H4h, H4fh, Hist1h4i, H4m, H4fm, Hist1h4j, H4fe, Hist1h4k, H4d, H4fd, Hist1h4l, H4k, H4fk, Hist2h4a, H4f2, H4fn, Hist2h4, Hist2h4b, H4o, H4fo, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2a.2,Histone H2aa,Histone H2am
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ab, H2afm, Hist1h2ae, H2afa
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-J
Chain: D, H
Synonym: Histone H2b.1,Histone H2b.R,H2br
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2bj, H2bfr
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.235 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.190 109.400 174.820 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand MG, RRK, RUD, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceNucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation., Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA, Nat Commun. 2017 Nov 17;8(1):1575. doi: 10.1038/s41467-017-01680-4. PMID:29146919
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (5xf3.pdb1.gz) 245 Kb
  • LPC: Ligand-Protein Contacts for 5XF3
  • CSU: Contacts of Structural Units for 5XF3
  • Structure Factors (2894 Kb)
  • Retrieve 5XF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XF3 from S2C, [Save to disk]
  • View 5XF3 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 5XF3
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xf3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xf3_H] [5xf3_B] [5xf3_D] [5xf3_F] [5xf3_G] [5xf3_A] [5xf3_C] [5xf3_E] [5xf3_J] [5xf3_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XF3
  • Community annotation for 5XF3 at PDBWiki (http://pdbwiki.org)

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