2YW8 Metal Binding Protein date Apr 20, 2007
title Crystal Structure Of Human Run And Fyve Domain-Containing Protein
authors H.Wang, S.Kishishita, K.Murayama, C.Takemoto, T.Terada, M.Shirouzu, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Run And Fyve Domain-Containing Protein 1
Chain: A
Fragment: Unp Residues 627-708
Synonym: Fyve-Finger Protein Eip1, Zinc Finger Fyve Domain- Containing Protein 12, La-Binding Protein 1, Rab4- Interacting Protein, Ms1309 Protein;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rufy1, Rabip4, Zfyve12
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pk060327-08
Other_details: Cell-Free Protein Synthesis
symmetry Space Group: P 43 3 2
R_factor 0.198 R_Free 0.224
length a length b length c angle alpha angle beta angle gamma
115.150 115.150 115.150 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand SO4, ZN enzyme
note 2YW8 is a representative structure

Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (16 Kb) [Save to disk]
  • Biological Unit Coordinates (2yw8.pdb1.gz) 12 Kb
  • LPC: Ligand-Protein Contacts for 2YW8
  • CSU: Contacts of Structural Units for 2YW8
  • Likely Quarternary Molecular Structure file(s) for 2YW8
  • Structure Factors (37 Kb)
  • Retrieve 2YW8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YW8 from S2C, [Save to disk]
  • Re-refined 2yw8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YW8 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 2YW8
  • 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 2YW8, from MSDmotif at EBI
  • Fold representative 2yw8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yw8] [2yw8_A]
  • SWISS-PROT database: [Q96T51]
  • Domain organization of [RUFY1_HUMAN] by SWISSPFAM
  • Domain found in 2YW8: [FYVE ] by SMART
  • Other resources with information on 2YW8
  • Community annotation for 2YW8 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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