1YB1 Oxidoreductase date Dec 18, 2004
title Crystal Structure Of Human 17-Beta-Hydroxysteroid Dehydrogen Xi
authors P.Lukacik, G.Bunkoczi, K.Kavanagh, S.Ng, F.Von Delft, J.Bray, A.Ed C.Arrowsmith, M.Sundstrom, U.Oppermann, Structural Genomics Co (Sgc)
compound source
Molecule: 17-Beta-Hydroxysteroid Dehydrogenase Type Xi
Chain: A, B
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dhrs8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta 2 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P11 (Pet11 Derivative)
symmetry Space Group: P 41 21 2
R_factor 0.162 R_Free 0.192
length a length b length c angle alpha angle beta angle gamma
110.939 110.939 118.013 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand AOI, CL, GOL, SO4 enzyme Oxidoreductase E.C. BRENDA
A, B

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1yb1.pdb1.gz) 83 Kb
  • Biological Unit Coordinates (1yb1.pdb2.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 1YB1
  • CSU: Contacts of Structural Units for 1YB1
  • Likely Quarternary Molecular Structure file(s) for 1YB1
  • Structure Factors (414 Kb)
  • Retrieve 1YB1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YB1 from S2C, [Save to disk]
  • Re-refined 1yb1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YB1 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 1YB1
  • 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 1YB1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1yb1a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1yb1b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1g1yb1, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1k1yb1, region B:311-384 [Jmol] [rasmolscript] [script source]
  • Fold representative 1yb1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yb1_A] [1yb1] [1yb1_B]
  • SWISS-PROT database: [Q8NBQ5]
  • Domain organization of [DHB11_HUMAN] by SWISSPFAM
  • Other resources with information on 1YB1
  • Community annotation for 1YB1 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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