1NK3 Dna Binding Protein Dna date May 06, 1998
title Vndnk-2 Homeodomaindna Complex, Nmr, Minimized Average Str
authors J.M.Gruschus, D.H.H.Tsao, L.H.Wang, M.Nirenberg, J.A.Ferretti
compound source
Molecule: Dna (5'-D(Tpgptpgptpcpapapgptpgpgpcp 3');
Chain: A
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Apcpapgpcpcpapcptptpgpapcp 3');
Chain: B
Engineered: Yes

Synthetic: Yes

Molecule: Homeobox Protein Vnd
Chain: P
Fragment: Homeodomain
Synonym: Vndnk-2 Homeodomain, Ventral Nervous System Defec Protein, Homeobox Protein Nk-2;
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Organ: Fruit
Gene: Potential
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pet11d
methodSolution NMR
related structures by homologous chain: 1NK2, 1QRY
Gene
Ontology
ChainFunctionProcessComponent
P


Primary referenceInteractions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity., Gruschus JM, Tsao DH, Wang LH, Nirenberg M, Ferretti JA, Biochemistry 1997 May 6;36(18):5372-80. PMID:9154919
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1nk3.pdb1.gz) 40 Kb
  • CSU: Contacts of Structural Units for 1NK3
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1NK3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NK3 from S2C, [Save to disk]
  • View 1NK3 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 1NK3
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NK3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nk3p_, region P [Jmol] [rasmolscript] [script source]
  • 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: [1nk3_A] [1nk3] [1nk3_P] [1nk3_B]
  • SWISS-PROT database: [P22808]
  • Domain organization of [VND_DROME] by SWISSPFAM
  • Domain found in 1NK3: [HOX ] by SMART
  • Other resources with information on 1NK3
  • Community annotation for 1NK3 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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