6PAX Gene Regulation Dna date Apr 22, 1999
title Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions
authors H.E.Xu, M.A.Rould, W.Xu, J.A.Epstein, R.L.Maas, C.O.Pabo
compound source
Molecule: 26 Nucleotide Dna
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 26 Nucleotide Dna
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Homeobox Protein Pax-6
Chain: A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pax6
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.233 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
33.840 61.686 171.111 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
related structures by homologous chain: 1K78, 1PDN
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding., Xu HE, Rould MA, Xu W, Epstein JA, Maas RL, Pabo CO, Genes Dev 1999 May 15;13(10):1263-75. PMID:10346815
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (6pax.pdb1.gz) 51 Kb
  • CSU: Contacts of Structural Units for 6PAX
  • Likely Quarternary Molecular Structure file(s) for 6PAX
  • Structure Factors (141 Kb)
  • Retrieve 6PAX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6PAX from S2C, [Save to disk]
  • Re-refined 6pax structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 6PAX 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 6PAX
  • 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 6PAX, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d6paxa1, region A:1-68 [Jmol] [rasmolscript] [script source]
        - Domain d6paxa2, region A:69-133 [Jmol] [rasmolscript] [script source]
  • Fold representative 6pax 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: [6pax_B] [6pax] [6pax_A] [6pax_C]
  • SWISS-PROT database: [P26367]
  • Domain organization of [PAX6_HUMAN] by SWISSPFAM
  • Domain found in 6PAX: [PAX ] by SMART
  • Alignments of the sequence of 6PAX with the sequences similar proteins can be viewed for 6PAX's classification [PAX6_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [PAX6_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 6PAX
  • Community annotation for 6PAX 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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