2YYO Structural Genomics, Unknown Function date Apr 30, 2007
title Crystal Sturcture Of Human Spry Domain
authors S.Kishishita, T.Uchikubo-Kamo, K.Murayama, T.Terada, L.Chen, Z.Q.Fu, J.Chrzas, M.Shirouzu, B.C.Wang, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Spry Domain-Containing Protein 3
Chain: A
Fragment: Spry Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Spryd3
Expression_system: Cell-Free Protein Synthesis
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pk050905-07
symmetry Space Group: P 43 21 2
R_factor 0.218 R_Free 0.261
crystal
cell
length a length b length c angle alpha angle beta angle gamma
52.107 52.107 108.583 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand MSE enzyme
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (2yyo.pdb1.gz) 53 Kb
  • Biological Unit Coordinates (2yyo.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 2YYO
  • CSU: Contacts of Structural Units for 2YYO
  • Likely Quarternary Molecular Structure file(s) for 2YYO
  • Structure Factors (137 Kb)
  • Retrieve 2YYO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YYO from S2C, [Save to disk]
  • Re-refined 2yyo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YYO 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 2YYO
  • 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 2YYO, from MSDmotif at EBI
  • Fold representative 2yyo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yyo] [2yyo_A]
  • SWISS-PROT database: [Q8NCJ5]
  • Domain organization of [SPRY3_HUMAN] by SWISSPFAM
  • Domain found in 2YYO: [SPRY ] by SMART
  • Other resources with information on 2YYO
  • Community annotation for 2YYO 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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