1PDN Gene Regulation Dna date May 16, 1995
title Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations
authors W.Xu, M.A.Rould, S.Jun, C.Desplan, C.O.Pabo
compound source
Molecule: Dna (5'- D(Apapcpgptpcpapcpgpgptptpgpapc)-3');
Chain: A
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Protein (Prd Paired)
Chain: C
Engineered: Yes

Organism_scientific: Drosophila Melanogaster
Organism_common: Fruit Fly
Organism_taxid: 7227
Gene: Prd
Expression_system: Bl21(De3)
Expression_system_common: Bl21(De3)
Expression_system_plasmid: Pet14bprdpdb
Expression_system_gene: Prd
symmetry Space Group: P 21 21 21
R_factor 0.234 R_Free 0.284
length a length b length c angle alpha angle beta angle gamma
39.600 68.600 100.500 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
related structures by homologous chain: 1MDM, 6PAX

Primary referenceCrystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations., Xu W, Rould MA, Jun S, Desplan C, Pabo CO, Cell 1995 Feb 24;80(4):639-50. PMID:7867071
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (1pdn.pdb1.gz) 31 Kb
  • CSU: Contacts of Structural Units for 1PDN
  • Likely Quarternary Molecular Structure file(s) for 1PDN
  • Retrieve 1PDN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PDN from S2C, [Save to disk]
  • View 1PDN 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 1PDN
  • 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 1PDN, from MSDmotif at EBI
  • Genome occurence of 1PDN's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pdnc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1pdn 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: [1pdn] [1pdn_A] [1pdn_C] [1pdn_B]
  • SWISS-PROT database: [P06601]
  • Domain organization of [PRD_DROME] by SWISSPFAM
  • Domain found in 1PDN: [PAX ] by SMART
  • Other resources with information on 1PDN
  • Community annotation for 1PDN 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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