1KX5 Structural Protein Dna date Jan 31, 2002
title X-Ray Structure Of The Nucleosome Core Particle, Ncp147, At 1.9 A Resolution
authors C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond
compound source
Molecule: Dna (5'(Atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctccatcaa Aaggcatgttcagctggaatccagctgaacatgccttttgatggagcagtttccaaata Cacttttggtagtatctgcaggtggatattgat)3');
Chain: I
Engineered: Yes
Other_details: Palindromic 147 Base Pair Dna Duplex With Exception Of Position 0;
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Dna Sequence Synthesized, Cloned, Multimerized, And Excised From Plasmid;

Molecule: Dna (5'(Atcaatatccacctgcagatactaccaaaagtgtatttggaaactgctccatcaa Aaggcatgttcagctggattccagctgaacatgccttttgatggagcagtttccaaata Cacttttggtagtatctgcaggtggatattgat)3');
Chain: J
Engineered: Yes
Other_details: Palindromic 147 Base Pair Dna Duplex With Exception Of Position 0;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Dna Sequence Synthesized, Cloned, Multimerized, And Excised From Plasmid;

Molecule: Histone H3
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a.1
Chain: C, G
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b.2
Chain: D, H
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.950 181.170 109.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.94 Å
ligand CL, MN enzyme
related structures by homologous chain: 1KX3, 1TZY
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceSolvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution., Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, J Mol Biol 2002 Jun 21;319(5):1097-113. PMID:12079350
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (347 Kb) [Save to disk]
  • Biological Unit Coordinates (1kx5.pdb1.gz) 338 Kb
  • LPC: Ligand-Protein Contacts for 1KX5
  • CSU: Contacts of Structural Units for 1KX5
  • Likely Quarternary Molecular Structure file(s) for 1KX5
  • Retrieve 1KX5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KX5 from S2C, [Save to disk]
    • View 1KX5 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 1KX5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1KX5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kx5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kx5b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kx5c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kx5d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1kx5e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1kx5f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1kx5g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1kx5h_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1kx5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1kx5_I] [1kx5] [1kx5_A] [1kx5_G] [1kx5_F] [1kx5_J] [1kx5_H] [1kx5_E] [1kx5_B] [1kx5_C] [1kx5_D]
  • SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 1KX5: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 1KX5
  • Community annotation for 1KX5 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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