1K61 Transcription Dna date Oct 14, 2001
title Matalpha2 Homeodomain Bound To Dna
authors J.Aishima, R.K.Gitti, J.E.Noah, H.H.Gan, T.Schlick, C.Wolberger
compound source
Molecule: 5'- D(Apcpaptpgptpapaptptpcpaptptptpapcpapcp Gpc)-3';
Chain: E
Engineered: Yes
Synthetic: Yes
Other_details: This Sequence Is Derived From The Ste6 Promoter Region, With The Mcm1 Binding Sites Removed.;

Molecule: 5'-D((5iu) Pgpcpgptpgptpapapaptpgpapaptptpapcpaptp G)-3';
Chain: F
Engineered: Yes

Synthetic: Yes
Other_details: This Sequence Is Derived From The Ste6 Promoter Region, With The Mcm1 Binding Sites Removed.;

Molecule: Mating-Type Protein Alpha-2
Chain: A, B, C, D
Fragment: Residues 132-191, Homeodomain
Synonym: Alpha-2 Repressor
Engineered: Yes

Synthetic: Yes
Other_details: The Sequence Naturally Occurs In Yeast. The Protein Was Synthesized By The Fmoc Method.
symmetry Space Group: P 1 21 1
R_factor 0.221 R_Free 0.277
length a length b length c angle alpha angle beta angle gamma
38.940 70.240 68.290 90.00 105.42 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 5IU enzyme
note 1K61 is a representative structure
related structures by homologous chain: 1MNM
A, D, C, B

Primary referenceA Hoogsteen base pair embedded in undistorted B-DNA., Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C, Nucleic Acids Res 2002 Dec 1;30(23):5244-52. PMID:12466549
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (64 Kb) [Save to disk]
  • Biological Unit Coordinates (1k61.pdb1.gz) 60 Kb
  • LPC: Ligand-Protein Contacts for 1K61
  • CSU: Contacts of Structural Units for 1K61
  • Likely Quarternary Molecular Structure file(s) for 1K61
  • Structure Factors (254 Kb)
  • Retrieve 1K61 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K61 from S2C, [Save to disk]
  • Re-refined 1k61 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K61 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 1K61
  • 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
  • 3D motif for 1K61, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k61a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1k61b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1k61c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1k61d_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1k61 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: [1k61_B] [1k61_E] [1k61_A] [1k61_C] [1k61_D] [1k61_F] [1k61]
  • SWISS-PROT database: [Q6B2C0]
  • Domain organization of [MTAL2_YEAST] by SWISSPFAM
  • Domain found in 1K61: [HOX ] by SMART
  • Other resources with information on 1K61
  • Community annotation for 1K61 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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