1UBD Transcription Dna date Oct 04, 1996
title Co-Crystal Structure Of Human Yy1 Zinc Finger Domain Bound To The Adeno-Associated Virus P5 Initiator Element
authors H.B.Houbaviy, A.Usheva, T.Shenk, S.K.Burley
compound source
Molecule: Dna (5'- D(Apgpgpgptpcptpcpcpaptptptptpgpapa Pgpcpg)-3');
Chain: A
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Protein (Yy1 Zinc Finger Domain)
Chain: C
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.330
length a length b length c angle alpha angle beta angle gamma
44.000 65.700 117.100 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme
Primary referenceCocrystal structure of YY1 bound to the adeno-associated virus P5 initiator., Houbaviy HB, Usheva A, Shenk T, Burley SK, Proc Natl Acad Sci U S A 1996 Nov 26;93(24):13577-82. PMID:8942976
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (1ubd.pdb1.gz) 37 Kb
  • LPC: Ligand-Protein Contacts for 1UBD
  • CSU: Contacts of Structural Units for 1UBD
  • Likely Quarternary Molecular Structure file(s) for 1UBD
  • Retrieve 1UBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1UBD from S2C, [Save to disk]
  • View 1UBD 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 1UBD
  • 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 1UBD, from MSDmotif at EBI
  • Genome occurence of 1UBD's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ubdc1, region C:295-322 [Jmol] [rasmolscript] [script source]
        - Domain d1ubdc2, region C:323-350 [Jmol] [rasmolscript] [script source]
        - Domain d1ubdc3, region C:351-380 [Jmol] [rasmolscript] [script source]
        - Domain d1ubdc4, region C:381-408 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ubd 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: [1ubd] [1ubd_C] [1ubd_B] [1ubd_A]
  • SWISS-PROT database: [P25490]
  • Domain organization of [TYY1_HUMAN] by SWISSPFAM
  • Domain found in 1UBD: [ZnF_C2H2 ] by SMART
  • Other resources with information on 1UBD
  • Community annotation for 1UBD 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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