1M1A Structural Protein Dna date Jun 18, 2002
title Ligand Binding Alters The Structure And Dynamics Of Nucleoso
authors R.K.Suto, R.S.Edayathumangalam, C.L.White, C.Melander, J.M.Gotte P.B.Dervan, K.Luger
compound source
Molecule: Palindromic 146 Base Pair Dna Fragment
Chain: I, J
Engineered: Yes
Synthetic: Yes

Molecule: Histone H3.2
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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet

Molecule: Histone H2b.1
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
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.719 109.196 177.353 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand ABU, BAL, DIB, IMT, MN, PYB enzyme
related structures by homologous chain: 1KX4, 1P3P
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceCrystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands., Suto RK, Edayathumangalam RS, White CL, Melander C, Gottesfeld JM, Dervan PB, Luger K, J Mol Biol 2003 Feb 14;326(2):371-80. PMID:12559907
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (1m1a.pdb1.gz) 247 Kb
  • LPC: Ligand-Protein Contacts for 1M1A
  • CSU: Contacts of Structural Units for 1M1A
  • Likely Quarternary Molecular Structure file(s) for 1M1A
  • Retrieve 1M1A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M1A from S2C, [Save to disk]
  • View 1M1A 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 1M1A
  • 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 1M1A, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m1aa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m1ab_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1m1ac_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m1ad_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m1ae_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1m1af_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1m1ag_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1m1ah_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1m1a 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: [1m1a_G] [1m1a_F] [1m1a_D] [1m1a_B] [1m1a] [1m1a_C] [1m1a_H] [1m1a_A] [1m1a_I] [1m1a_E] [1m1a_J]
  • SWISS-PROT database: [P06897] [P02281] [P02302] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H3L_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 1M1A: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 1M1A
  • Community annotation for 1M1A 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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